Hi Justin,
No. I have not added any ions.
Samrat
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Sent: Friday, October 21, 2011 11:39 AM
Subject: Re: [gmx-users] mismatch in coordinate and topology
Samrat Pal wrote:
> Hi Justin,
>
.
Samrat
From: Justin A. Lemkul
To: Samrat Pal ; Discussion list for GROMACS users
Sent: Friday, October 21, 2011 8:49 AM
Subject: Re: [gmx-users] mismatch in coordinate and topology
Samrat Pal wrote:
> Hi All,
> I am trying to minimi
Hi All,
I am trying to minimize the chryptochrome structure that has one FAD
and one MHF ligand bound to it.
Following are the steps that I performed
(1) Created the protein coordinate(gro) file using pdb2gmx command and choosing
GROMOS43a1 force-field
(2) Created the FAD and
Hi All,
Is it possible to use thermodynamic integration method with implicit
solvent model in gromacs 4.5.4?
Thanks
Samrat--
gmx-users mailing listgmx-users@gromacs.org
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Please search the archive at
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Oh! Thanks a lot.
Samrat
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Sent: Mon, November 15, 2010 6:16:51 PM
Subject: Re: [gmx-users] compressing two selections or just the reverse of
pulling simulation
Samrat Pal wrote:
> Hi
Hi All,
In general what we do in pulling simulations that we pull one
selection keeping the other fixed. In that case the distance between the two
selections increases with time. Now, I want to push the selections i.e. one
selection will be kept fixed and the other will be pushed towa
pull_k1 = 1000
I have given pull_dim Y Y Y as I am not pulling in a particular direction. Is
it
right?
From: Samrat Pal
To: jalem...@vt.edu; Discussion list for GROMACS users
Sent: Sat, August 14, 2010 11:00:37 AM
Subject: Re: [gmx-users] negative
Thanks a lot.
Best
Samrat
From: Justin A. Lemkul
To: Gromacs Users' List
Sent: Sat, August 14, 2010 10:50:05 AM
Subject: Re: [gmx-users] negative values of force
Samrat Pal wrote:
> (1) I have got the pull.xvg file from the simulation. But there
emkul
To: Discussion list for GROMACS users
Sent: Sat, August 14, 2010 10:34:25 AM
Subject: Re: [gmx-users] negative values of force
Samrat Pal wrote:
> Dear All,
> I have pulled a protein by keeping n-terminus fixed and pulling
>the c-terminus. I tried to extract
Dear All,
I have pulled a protein by keeping n-terminus fixed and pulling
the c-terminus. I tried to extract the force.xvg profile from the .trr file by
the following command -
g_traj -f traj.trr -s pull.tpr -of force.xvg
But in the force.xvg profile I am getting both positive and
Hi all,
Can anyone please give me a mdp file for running pulling simulations
in implicit solvent using GROMACS?
Thanks in advance
Samrat
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www
-users] abnormal stop of job
On Thu, Aug 5, 2010 at 1:37 PM, Samrat Pal wrote:
>
> Received the TERM signal, stopping at the next step
The TERM signal is the default signal sent by the command "kill" to
stop a job. Pressing Ctrl-C while the program is running on the
foreground has
Hi all,
I have been running a simulation of 200 ns length and it suddenly
stoped at 67 ns showing the following line -
Received the TERM signal, stopping at the next step
I have checked the time steps properly and there is no error. What should I do
now? Please suggest.
Thanks
Samr
in the conventional way?
Please suggest.
Thanks
Samrat Pal
From: Samrat Pal
To: Discussion list for GROMACS users
Sent: Tue, July 27, 2010 2:59:01 PM
Subject: Jarzynski equality in pulling simulation
Dear All,
I am trying to do unfolding
) running multiple trajectories and apply Jarzynski equality to get free
energy
OR
(2) running a single trajectory and taking configurations at different
distances
and then apply umbrella sampling to compute PMF.
Please advise.
Thanks in advance,
Samrat Pal
run simulations using
implicit water model (GB or something)? If that so, then please anyone give me
a
model .mdp file or any input file where the option for implcit model can be
given.
Samrat Pal
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gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman
?
Samrat.
From: Samrat Pal
To: jalem...@vt.edu; Discussion list for GROMACS users
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
Another thing is that I am not sure how to get the force-extension profile from
the simulation trajectory?
Thanks
Samrat
From: Samrat Pal
To: jalem...@vt.edu; Discussion list for GROMACS users
Sent: Sun, July 18, 2010 12:21:04 PM
Subject: Re: [gmx-users
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
Hey,.. Thank you for the script. I will keep in mind what you said next time.
Samrat Pal
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Sent: Fri, July 16, 2010 5:18:44 PM
Subject: Re: [gmx-users] Need For a Script
Samrat Pal wrote:
> D
script for that so that
I
can standardise my protocol? Suggestion is urgent.
Thanks in advance
Samrat Pal
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