[gmx-users] Need For a Script

[Samrat Pal]

Hi Justin,
    I am trying to perform umbrella sampling following your link. But when I put 
the command
grompp -f md_umbrella.mdp -c conf0.gro -p topol.top -n index.ndx -o 
umbrella0.tpr

I found the the following error

No molecules were defined in the system

Could you please suggest please?

Samrat.






________________________________
From: Samrat Pal <psamrat10 at yahoo.com>
To: jalemkul at vt.edu; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Mon, July 19, 2010 10:00:27 AM
Subject: Re: [gmx-users] Need For a Script


Another thing is that I am not sure how to get the force-extension profile from 
the simulation trajectory? 

Thanks
Samrat  




________________________________
From: Samrat Pal <psamrat10 at yahoo.com>
To: jalemkul at vt.edu; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Sun, July 18, 2010 12:21:04 PM
Subject: Re: [gmx-users] Need For a Script


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.
Thanks in advance
Samrat Pal 




________________________________
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Fri, July 16, 2010 5:18:44  PM
Subject: Re: [gmx-users] Need For a Script



Samrat Pal wrote:
> Dear All,
>     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.

http://www.gromacs.org/Documentation/Tutorials#Umbrella_Sampling

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.

-Justin

>    Thanks in advance
> Samrat Pal
> 

-- ========================================

Justin A. Lemkul
Ph.D.  Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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