Does anyone has a clear definition or a reference for the Twin-range cut-off? I
searched the internet and looked at the manual yet I couldn't get the idea
Thanks Rabab Toubar
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Hi
I was wondering if there is a way to determine the water box size from the
output files after the simulation run is over
Thanks
Rabab Toubar
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Thanks Justin for your reply. But what is the extension of the output
coordinate file. And for the .edr file it failed to open in windows; how can I
possibly view it
Thanks
Rabab Toubar
--- On Mon, 7/25/11, Justin A. Lemkul jalem...@vt.edu wrote:
From: Justin A. Lemkul jalem...@vt.edu
to confirm that the
molecule is properly reduced
Rabab Toubar
--- On Wed, 8/25/10, Mark Abraham mark.abra...@anu.edu.au wrote:
From: Mark Abraham mark.abra...@anu.edu.au
Subject: Re: [gmx-users] How to tell if the molecule is correctly reduced?
To: Discussion list for GROMACS users gmx-users
Hi
I did simulations for a protein with disulfide bonds using opls. Then I reduced
the ssbonds in vmd and did simulations for the reduced. When loading gro(or
pdb) and trr files on vmd I do not see reduced bonds. I also compared the two
pdb files and they looked the same in terms of number of
Hi,
I want to extract the values for potential E, kinetic E, total E, and
temperature from the log file so as to plot them versus time. In NAMD it is
easy to do that using cat |grep, is there a similar way to do it in GMX
Thanks
Rabab Toubar
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gmx-users mailing listgmx-users
So is there a way we can make His neutral before running the simulations as in
case of NAMD?
Rabab Toubar
--- On Wed, 6/16/10, Justin A. Lemkul jalem...@vt.edu wrote:
From: Justin A. Lemkul jalem...@vt.edu
Subject: [gmx-users] Re: His protonation
To: sagar barage sagarbar...@gmail.com
I have noticed that you get the overall charge WHILE you are setting up the
system - when using grompp I think. Now if after the mdrun and I want to check
the overall charge, how can I possibly do that?
I tried the mailing list but didn't find an answer to my question
Thanks
Rabab Toubar
Hi,
I want to extract the protein only without the waters. And from the mailing
list discussing trjconv, what I did was:
make_ndx -f conf-protein
trajconv -f pr.trr -n index.ndx -o pr_trj.trr
, but I get file input/output error
Am I missing something?
Thanks
Rabab Toubar
--- On Tue, 6/15
Rabab Toubar
--- On Wed, 6/16/10, Justin A. Lemkul jalem...@vt.edu wrote:
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] trjconv index file
To: Discussion list for GROMACS users gmx-users@gromacs.org
Date: Wednesday, June 16, 2010, 7:26 AM
Rabab Toubar wrote:
Hi
I came across this paper for the ff G45a3 and it says that is good for
aliphatics, so I was wondering if there is a forcefield that is recommended to
be used in case of proteins simulations in water.
Rabab Toubar
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gmx-users mailing listgmx-users@gromacs.org
http
Trying to extract the protein from the md run without waters, all the mailing
lists suggests using an index file
before running trjconv, but I get file input/output error
Can someone give me more details on how to egt the index
file
thanks
Rabab
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gmx-users mailing list
Hi
Trying to use top2psf.pl, as suggested
Usage: top2psf.pl -i (topology filename) -o (output filename)
but I get an error message saying
invalid command name top2psf.pl
Suggestions?
Thanks
Rabab
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gmx-users mailing listgmx-users@gromacs.org
Hi,
Can anyone let me know how to know how long the md run would take, or how long
is left. I tried tailing it, but couldn't find a time factor there
Thanks
Rabab
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Please search the
= 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 621432
Any suggestions are appreciated
Thanks
Rabab Toubar
--- On Thu, 6/3/10, Justin A. Lemkul jalem...@vt.edu wrote:
From: Justin A. Lemkul jalem...@vt.edu
well till the end of the 25 ns run! But seems that mine is
crashing. Any suggestions?
Thanks
Rabab Toubar
--- On Fri, 6/4/10, Justin A. Lemkul jalem...@vt.edu wrote:
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] 1-4 interaction not within cut-off
To: Gromacs Users' List gmx
, and the simulations were carried out.
Thanks
Rabab Toubar
--- On Fri, 6/4/10, Justin A. Lemkul jalem...@vt.edu wrote:
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] 1-4 interaction not within cut-off
To: Gromacs Users' List gmx-users@gromacs.org
Date: Friday, June 4, 2010, 3
Hi,
I set my .mdp file to minimize the system for 1000 steps, but it stopped at
~200 saying: Stepsize too small, or no change in energy.
Converged to machine precision, but not to the requested precision Fmax 10
but the molecule is now outside the box
I did position restraint for 2ns using
if we define
-DPOSRES
My question is the run ended very quickly that doesn't seem 2ns for me. I
apologize if it is a silly question but I have just strated using GMX
Thanks
Rabab Toubar
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