<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt">Hi Justin,<br> I am trying to perform umbrella sampling following your link. But when I put the command<br><font face="Arial"><font size="3"><pre>grompp -f md_umbrella.mdp -c conf0.gro -p topol.top -n index.ndx -o umbrella0.tpr<br><br>I found the the following error<br><br>No molecules were defined in the system<br><br>Could you please suggest please?<br><br>Samrat.<br></pre></font></font><br><div><br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Samrat Pal <psamrat10@yahoo.com><br><b><span style="font-weight: bold;">To:</span></b> jalemkul@vt.edu;
Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Mon, July 19, 2010 10:00:27 AM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Need For a Script<br></font><br>
<meta http-equiv="x-dns-prefetch-control" content="off"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div>Another thing is that I am not sure how to get the force-extension profile from the simulation trajectory? <br>Thanks<br>Samrat <br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Samrat Pal <psamrat10@yahoo.com><br><b><span style="font-weight: bold;">To:</span></b> jalemkul@vt.edu; Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Sun, July 18, 2010 12:21:04 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Need For a Script<br></font><br>
<div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div>I have been doing the pull simulations with your scripts and that are running fine. Thanks a lot. Can I use implicit solvent model in pulling simulations? I have gone through the mailing list and I found that it is not recommended (I may be wrong). Please suggest.<br>Thanks in advance<br>Samrat Pal <br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br><div style="font-family: arial,helvetica,sans-serif; font-size: 13px;"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Justin A. Lemkul <jalemkul@vt.edu><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Fri, July 16, 2010 5:18:44
PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Need For a Script<br></font><br>
<br><br>Samrat Pal wrote:<br>> Dear All,<br>> I am a new GROMACS user. I have been able to solvate a protein in a water box and also to simulate it and unfold it by heating it. But I have facing problem with the script of AFM pulling. I want to unfold a protein by pulling the two ends of the protein. Can anyone give me a full script for that so that I can standardise my protocol? Suggestion is urgent.<br><br><span><span><span><a target="_blank" href="http://www.gromacs.org/Documentation/Tutorials#Umbrella_Sampling">http://www.gromacs.org/Documentation/Tutorials#Umbrella_Sampling</a></span></span></span><br><br>Also, as a bit of advice, don't use the word "urgent" when asking for free help. You're hoping someone else (who is busy) will find time to solve an issue for you.<br><br>-Justin<br><br>> Thanks in advance<br>> Samrat Pal<br>> <br><br>-- ========================================<br><br>Justin A.
Lemkul<br>Ph.D.
Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]<a rel="nofollow" target="_blank" href="http://vt.edu">vt.edu</a> | (540) 231-9080<br><span><span><span><a target="_blank" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a></span></span></span><br><br>========================================<br>-- gmx-users mailing list <a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><span><span><span><a target="_blank" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a></span></span></span><br><span><span><span>Please search the archive at <a target="_blank" href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before
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