<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252">
<style type="text/css" style="display:none;"> P {margin-top:0;margin-bottom:0;} </style>
</head>
<body dir="ltr">
<div class="elementToProof" style="font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Dear AMBER developers:</div>
<div class="elementToProof" style="font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div class="elementToProof" style="font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
I am interested in clarifying what exactly is happening when I follow the constant PH tutorial and use pmemd.cuda. My two questions are following:</div>
<div class="elementToProof" style="font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<ol start="1" style="margin-top: 0px; margin-bottom: 0px; list-style-type: decimal;" data-editing-info="{"applyListStyleFromLevel":false,"orderedStyleType":1}">
<li style="font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<div class="elementToProof" role="presentation"> What is the difference between the two manners of passing in parameters for running constant PH simulations?</div>
</li></ol>
<div class="elementToProof" style="font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div class="elementToProof" style="font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
There is method 1 (Constant PH tutorial approach <a href="https://ambermd.org/tutorials/advanced/tutorial18/" id="OWA019c3a1e-e9d5-e7e0-e0e7-b0b8b3794001" class="OWAAutoLink">
https://ambermd.org/tutorials/advanced/tutorial18/</a>)</div>
<div class="elementToProof" style="font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
TLEAP</div>
<div class="elementToProof" style="font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
"source leaprc.constph"</div>
<div style="line-height: 19px; font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
command line (e.g., AS4/GL4 dihedrals)</div>
<div style="line-height: 19px; font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
cpinutil.py -resnames HIP GL4 AS4 -p protein.prmtop -o protein.cpin</div>
<div style="line-height: 19px; font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
pmemd.cuda [...] -cpin cpin_file.in -cpout protein.prod.cpout -cprestrt protein.prod.cprestrt</div>
<div style="line-height: 19px; font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
<br>
</div>
<div style="line-height: 19px; font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
Method 2 (GBNECK Patch Shen Lab Approach<a href="https://gitlab.com/shenlab-amber-cphmd" id="LPlnk921966" class="OWAAutoLink"> https://gitlab.com/shenlab-amber-cphmd</a>)</div>
<div style="line-height: 19px; font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
TLEAP</div>
<div style="line-height: 19px; font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
# Load the ff14SB force field</div>
<div style="line-height: 19px; font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
source leaprc.protein.ff14SB</div>
<div style="line-height: 19px; font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
<br>
</div>
<div style="line-height: 19px; font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
# Set PBradii to mbondi3 (required for GBNeck2 in CpHMD)</div>
<div style="line-height: 19px; font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
set default PBradii mbondi3</div>
<div style="line-height: 19px; font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
<br>
</div>
<div style="line-height: 19px; font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
# Load the CpHMD residue definitions (AS2 and GL2)</div>
<div style="line-height: 19px; font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
loadoff phmd.lib</div>
<div style="line-height: 19px; font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
<br>
</div>
<div style="line-height: 19px; font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
# Load force field modifications for CpHMD (e.g., AS2/GL2 dihedrals)</div>
<div style="line-height: 19px; font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
loadamberparams frcmod.phmd</div>
<div style="line-height: 19px; font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
<br>
</div>
<div style="line-height: 19px; font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
pmemd.cuda [...] -cpout protein.prod.cpout -cprestrt protein.prod.cprestrt \</div>
<div style="line-height: 19px; font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
-phmdparm gbneck2_input.parm -phmdin ph.mdin -phmdout protein.prod.lam -phmdrestrt protein.prod.phmdrst</div>
<div style="line-height: 19px; font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
<br>
</div>
<div class="elementToProof" style="font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<ol start="2" style="margin-top: 0px; margin-bottom: 0px; list-style-type: decimal;" data-editing-info="{"applyListStyleFromLevel":false,"orderedStyleType":1}">
<li style="font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<div class="elementToProof" role="presentation">How much of the calculation is on the GPU? Are implicit solvent constant PH simulations accurate when using pmemd.cuda?</div>
</li></ol>
<div class="elementToProof" style="font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div class="elementToProof" style="font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Continuous constant pH MD can be performed in three modes: implicit solvent (iphmd=1, only available in</div>
<div class="elementToProof" style="font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
CPU),[676–678] hybrid solvent (iphmd=2),[679] and all-atom (iphmd=3). [680–682] In the implicit-solvent mode,</div>
<div class="elementToProof" style="font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
both conformational and protonation state sampling is performed using a generalized Born (GB) model. [...]
<i>The implicit-solvent mode makes uses of the GBNeck2 model[28], and it is implemented for both CPUs[677] and GPUs[678], although the GPU version is currently only available through a downloadable patch (https://gitlab.com/shenlab-amber-cphmd/cphmd-patches).</i> By
contrast, the all-atom mode (iphmd=3) is implemented only for GPUs.[682]</div>
<div class="elementToProof" style="font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div class="elementToProof" style="font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Thank you in advance for your time,</div>
<div class="elementToProof" style="font-family: Aptos, "Aptos_EmbeddedFont", "Aptos_MSFontService", Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Greg</div>
</body>
</html>