[gmx-users] Re: gmx-users Digest, Vol 92, Issue 138
Zahra M
s_zahra_mousavi at yahoo.com
Thu Dec 29 21:35:19 CET 2011
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To: gmx-users at gromacs.org
Sent: Thursday, December 29, 2011 1:05 PM
Subject: gmx-users Digest, Vol 92, Issue 138
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Today's Topics:
1. Re: -pbc nojump (mohammad agha)
2. positive potential energy (Zahra
M)
3. Re: positive potential energy (Zahra M)
4. Re: Re: positive potential energy (Mark Abraham)
----------------------------------------------------------------------
Message: 1
Date: Wed, 28 Dec 2011 18:54:54 -0800 (PST)
From: mohammad agha <mra_bu at yahoo.com>
Subject: Re: [gmx-users] -pbc nojump
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Message-ID:
<1325127294.34356.YahooMailNeo at web125705.mail.ne1.yahoo.com>
Content-Type: text/plain;
charset="us-ascii"
Thank you very much from your reply.
Best Regards
Sara
________________________________
From: Tsjerk Wassenaar <tsjerkw at gmail.com>
To: mohammad agha <mra_bu at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Thursday, December 29, 2011 1:56 AM
Subject: Re: [gmx-users] -pbc nojump
Hi Sara,
Please keep discussions on the list. I'm not your private tutor.
Whether you can do your analysis depends on the analysis you want to
do. But if your aim is analyzing the formation of the micelle, you're
probably better of reversing the trajectory.
> 1- trjconv -f md.trr -o md1.xtc -n index.ndx -pbc whole
-s md.tpr
This makes molecules whole, which is fine. Clustering should make
molecules whole too, though, making this step redundant.
> 2- trjconv -f md1.xtc -s md.tpr -o cluster1.gro -e 600000 -pbc cluster
Fine, you get a cluster
> 3- trjconv -f cluster1.gro -s md.tpr -dump 150 -o cluster2.gro
This does nothing special. Just because you have a reference clustered
doesn't mean the output frame will turn out clustered.
> 4- grompp -f md.mdp -c cluster2.gro -o cluster1.tpr -n index.ndx
> 5- trjconv -f cluster1.gro -o cluster1.xtc -s cluster1.tpr -pbc nojump
This screws up everything. You can only use -pbc nojump with a
reference structure that is sufficiently close to the first frame of
the trajectory. Your reference is a snapshot at t=600 ns.
> 6- trjconv -f cluster1.xtc -s cluster1.tpr -pbc mol -ur compact -center -o
> cluster3.xtc
This would probably be
fine if the trajectory was okay there.
Cheers,
Tsjerk
--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Message: 2
Date: Thu, 29 Dec 2011 01:22:15 -0800 (PST)
From: Zahra M <s_zahra_mousavi at yahoo.com>
Subject: [gmx-users] positive potential energy
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
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<1325150535.62665.YahooMailNeo at web161705.mail.bf1.yahoo.com>
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Hi dear all
I'm simulating a system containing CNT, when I put CNT in a unit cell and want to run energy minimization in a vacuum, I encounter with such an error: "The optimal PME mesh load for parallel simulations is below 0.5 and
for highly parallel simulations between 0.25 and 0.33, for higher
performance, increase the cut-off and the PME grid spacing", after running grompp. I've tried a lot of numbers for cut-off radius ,but I didn't get any result, at last I changed the coulomb type from PME to Cut-off, and it worked, I want to know if my
results will be reasonable in this case or not, and how to solve that error.
thank you in advanced
Bests
-Zahra
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Message: 3
Date: Thu, 29 Dec 2011 01:24:14 -0800 (PST)
From: Zahra M <s_zahra_mousavi at yahoo.com>
Subject: [gmx-users] Re: positive potential energy
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Message-ID:
<1325150654.64323.YahooMailNeo at web161705.mail.bf1.yahoo.com>
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Sorry ...I forget to announce that my potential energy is positive, is it logical?
________________________________
From: Zahra M <s_zahra_mousavi at yahoo.com>
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Sent: Thursday, December 29, 2011 12:52 PM
Subject: positive potential
energy
Hi dear all
I'm simulating a system containing CNT, when I put CNT in a unit cell and want to run energy minimization in a vacuum, I encounter with such an error: "The optimal PME mesh load for parallel simulations is below 0.5 and
for highly parallel simulations between 0.25 and 0.33, for higher
performance, increase the cut-off and the PME grid spacing", after running grompp. I've tried a lot of numbers for cut-off radius ,but I didn't get any result, at last I changed the coulomb type from PME to Cut-off, and it worked, I want to know if my results will be reasonable in this case or not, and how to solve that error.
thank you in advanced
Bests
-Zahra
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Message: 4
Date: Thu, 29 Dec 2011 20:34:59 +1100
From: Mark Abraham <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] Re: positive potential energy
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4EFC3443.8060301 at anu.edu.au>
Content-Type: text/plain; charset="iso-8859-1"
On 29/12/2011 8:24 PM, Zahra M wrote:
> Sorry ...I forget to announce that my potential energy is positive, is
> it logical?
No.
>
>
------------------------------------------------------------------------
> *From:* Zahra M <s_zahra_mousavi at yahoo.com>
> *To:* "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> *Sent:* Thursday, December 29, 2011 12:52 PM
> *Subject:* positive potential energy
>
> Hi dear all
> I'm simulating a system containing CNT, when I put CNT in a unit cell
> and want to run energy minimization in a vacuum, I encounter with such
> an error: "The optimal PME mesh load for parallel simulations is below
> 0.5 and for highly parallel simulations between 0.25 and 0.33, for
> higher performance, increase the cut-off and the
PME grid spacing",
> after running grompp. I've tried a lot of numbers for cut-off radius
> ,but I didn't get any result, at last I changed the coulomb type from
> PME to Cut-off, and it worked, I want to know if my results will be
> reasonable in this case or not, and how to solve that error.
It's not an error, but an advisory about your performance, and doesn't
matter for EM in vacuo which will only run for a few seconds. Using a
plain cut-off is unreasonable by definition, but doesn't matter for EM
in vacuo. Otherwise, you should note that the suggestion is to "increase
the cut-off *and* the PME grid spacing," not just one of them.
Mark
Hi dear Mark
Thank you for your quick response.
I increased both of the grid spacing and cut-off, and it worked.
thank you very much...
-Zahra
> thank you in advanced
> Bests
>
> -Zahra
>
>
>
>
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