<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#ffffff">
On 28/01/2011 8:45 PM, Kwee Hong wrote:
<blockquote cite="mid:45763.27542.qm@web31401.mail.mud.yahoo.com"
type="cite">
<style type="text/css"><!-- DIV {margin:0px;} --></style>
<div style="font-family: arial,helvetica,sans-serif; font-size:
10pt; color: rgb(0, 0, 0);">
<div>
<div style="color: rgb(0, 0, 0); font-family:
arial,helvetica,sans-serif; font-size: 10pt;">Hi</div>
<div style="color: rgb(0, 0, 0); font-family:
arial,helvetica,sans-serif; font-size: 10pt;"><br>
</div>
In John's "GROMACS tutorial for solvation study of spider
toxin peptide",I keep on getting an error message at the
production stage: <br>
<br>
<br>
Step 12111 Warning: Pressure scaling more than 1%.<br>
<br>
Step 12121 Warning: Pressure scaling more than 1%.<br>
<br>
Step 12131 Warning: Pressure scaling more than 1%.<br>
<br>
-------------------------------------------------------<br>
Program mdrun, VERSION 4.5.1<br>
Source code file: ns.c, line: 2544<br>
<br>
Fatal error:<br>
One of the box vectors has become shorter than twice the
cut-off length or box_yy-|box_zy| or box_zz has become smaller
than the cut-off.<br>
For more information and tips for troubleshooting, please
check the GROMACS<br>
<span>website at <a moz-do-not-send="true" target="_blank"
href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a></span><br>
<br>
I've tried a few approaches after reading the mailing list yet
I'm still getting the same error message.<br>
<br>
The command lined I used in this simulation is as follow:<br>
pdb2gmx -ignh -ff gtomos43a1 -f 1OMB.pdb -o fws.pdb -p fws.top
-water spce<br>
</div>
</div>
</blockquote>
<br>
Typo there.<br>
<br>
<blockquote cite="mid:45763.27542.qm@web31401.mail.mud.yahoo.com"
type="cite">
<div style="font-family: arial,helvetica,sans-serif; font-size:
10pt; color: rgb(0, 0, 0);">
<div>editconf -bt cubic -f fws.pdb -o fws.pdb -d 1.0<br>
grompp -f em.mdp -c fws.pdb -p fws.top -o em.tpr -maxwarn 5<br>
mdrun -v -deffnm em<br>
grompp -f md.mdp -c em.gro -p fws.top -o md.tpr -maxwarn 3<br>
mdrun -v -deffnm md<br>
</div>
</div>
</blockquote>
<br>
Look at those warnings. Unless you know what they are and why
ignoring them is OK, don't use -maxwarn.<br>
<br>
<blockquote cite="mid:45763.27542.qm@web31401.mail.mud.yahoo.com"
type="cite">
<div style="font-family: arial,helvetica,sans-serif; font-size:
10pt; color: rgb(0, 0, 0);">
<div><br>
After getting the error above round step 2300, I increased the
tau_p from 0.5 to 1.0.<br>
<br>
Yet I got the same error message at step 5400 though the
warning on pressure scaling more than 1% was gone. <br>
Therefore, I inceased the -d option in editconf to 1.5.<br>
<br>
But once again, I got the same error message at step 7300 (no
warning on pressure scaling). <br>
So once again, I increased the -d option in editconf to 2.5.<br>
<br>
And I still got the same error message at step 11300.<br>
<br>
I'm now real lost in solving this.. I hereby attach my
full.mdp file, hopefully to get some insight here.<br>
Any suggestions are appreciated.<br>
</div>
</div>
</blockquote>
<br>
.mdp file looks OK.<br>
<br>
Mark<br>
<br>
<blockquote cite="mid:45763.27542.qm@web31401.mail.mud.yahoo.com"
type="cite">
<div style="font-family: arial,helvetica,sans-serif; font-size:
10pt; color: rgb(0, 0, 0);">
<div><br>
Thanks.<br>
<br>
Regards,<br>
Joyce<br>
<br>
<br>
</div>
</div>
<br>
</blockquote>
<br>
</body>
</html>