Very frequently it helps just to do some searches by your own and read
_carefully_ the documentation:
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations?highlight=extend
On 02/14/2013 08:13 AM, James Starlight wrote:
Dear Gromacs Users!
I have completed 100ns md trajectory.
I've already tried to do it in accordance to that instructions!
firstly I've created new tpr file where I changed only duration of my simulation
grompp -f ./mdps/md_sd.mdp -n index -c old.tpr -o new.tpr
then I've launched mdrun
mdrun -v -s new.tpr -cpi old.cpi -deffnm old -append
where old
It's all about comprehending reading. If you look carefully at the
documentation again, you will find:
tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr -cpi previous.cpt
What it's the right thing to do.
On 02/14/2013 10:11 AM, James Starlight wrote:
I've already
Dear users,
How can I get the number of interactions of each residue
within a cut off as a function of time. just like g_saltbr writes
with the option -sep.
I tried using g_mdmat but it gives an average contact map.
Thank you
Kavya
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gmx-users mailing listgmx-users@gromacs.org
Felipe,
thats works perfect! thank you!
James
2013/2/14 Felipe Pineda, PhD luis.pinedadecas...@lnu.se:
It's all about comprehending reading. If you look carefully at the
documentation again, you will find:
tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr -cpi
Thank the documentation, which you should probably read more carefully
the next time. Reading comprehension and discrete thinking are key.
On 02/14/2013 10:59 AM, James Starlight wrote:
Felipe,
thats works perfect! thank you!
James
2013/2/14 Felipe Pineda, PhD luis.pinedadecas...@lnu.se:
Perhaps g_hbond -contact will do what you want.
Erik
On Feb 14, 2013, at 10:42 AM, Kavyashree M wrote:
Dear users,
How can I get the number of interactions of each residue
within a cut off as a function of time. just like g_saltbr writes
with the option -sep.
I tried using g_mdmat but it
Thank you!
On Thu, Feb 14, 2013 at 3:38 PM, Erik Marklund er...@xray.bmc.uu.se wrote:
Perhaps g_hbond -contact will do what you want.
Erik
On Feb 14, 2013, at 10:42 AM, Kavyashree M wrote:
Dear users,
How can I get the number of interactions of each residue
within a cut off as a
Dear Stephane Abel,
Theres a link I on the gromacs web site to ATB, or you can google it. If it is
not in Gromacs format you can just write a couple 6 liner scripts to re-format
it by parsing into the gromacs format,
Stephan Watkins
Original-Nachricht
Datum: Wed, 13 Feb
You can use VideoMach software for this purpose. this software recommended by
VMD.
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Hello,
I am writing just to tell how the problem was solved.
I contact a person that works with the BlueGene cluster and he installed
the Gromacs 4.6 in the cluster.
And all my problems were solved. I did not get the same error over and
over again.
Apparently, it was some problem with the
Hello,
Yeap, I have seen the links on ATB. Indeed, the conversion of the bonded
terms (in this file 54a8.ifp ?) will be not too hard, but it is not the case
for the AA topology where several changes were done.
So any help will be appreciate..
Stephane
--
Hi,
There are two scripts make_gromos_rtp in the scripts directory which were used
to convert Gromos AA topologies to rtp entries.
Cheers,
Berk
From: stephane.a...@cea.fr
To: gmx-users@gromacs.org
Date: Thu, 14 Feb 2013 11:34:59 +
Subject:
On 2/13/13 5:23 PM, Steven Neumann wrote:
On Tue, Feb 12, 2013 at 5:01 PM, Justin Lemkul jalem...@vt.edu wrote:
On 2/12/13 9:57 AM, Steven Neumann wrote:
On Tue, Feb 12, 2013 at 2:53 PM, Justin Lemkul jalem...@vt.edu wrote:
On 2/12/13 9:40 AM, Steven Neumann wrote:
Dear Gmx Users,
On 2/14/13 1:01 AM, Алексей Раевский wrote:
Hi, dear developers!
I want to ask you abou dynamics in implicit solvent. I have a complex of
animal protein - dimer/trimer. After modeling by homology I have built
another one from the plant organism. Dimer/trimer was constructed with
superposition
On 2/14/13 1:20 AM, Ansuman Biswas wrote:
Original Message
Subject: Re: gmx-users Digest, Vol 106, Issue 68
From:ansuman@localhost
Date:Thu, February 14, 2013 10:16 am
To: gmx-users@gromacs.org
On 2/14/13 8:35 AM, Divya Sunil wrote:
Hello all,
I have been trying to apply distance restraints on my protein. I prepared
distance restrains using make index and added to topology file. I did it
just after executing pdb2gmx. Is this the correct procedure to apply
distance restraints?
Thanks Berk,
I have found the script, I will try them
Best
Stephane
Message: 4
Date: Thu, 14 Feb 2013 13:53:56 +0100
From: Berk Hess g...@hotmail.com
Subject: RE: [gmx-users] Re: GROMOS54A8 parameters in GROMACS format
To: Discussion list for GROMACS
On Feb 14, 2013, at 2:01 PM, Justin Lemkul wrote:
On 2/13/13 5:23 PM, Steven Neumann wrote:
On Tue, Feb 12, 2013 at 5:01 PM, Justin Lemkul jalem...@vt.edu
wrote:
On 2/12/13 9:57 AM, Steven Neumann wrote:
On Tue, Feb 12, 2013 at 2:53 PM, Justin Lemkul jalem...@vt.edu
wrote:
On
Erik, thanks for your answer. I typed which mdrun and I got this output:
*~$ which mdrun*
*/usr/local/gromacs/bin/mdrun*
Then, I typed just mdrun and I got this:
*~$ mdrun*
* *
* :-) G R O M A C S (-:*
*
*
* Green Red Orange Magenta Azure Cyan
On 2/14/13 9:40 AM, David Sáez wrote:
Erik, thanks for your answer. I typed which mdrun and I got this output:
*~$ which mdrun*
*/usr/local/gromacs/bin/mdrun*
Then, I typed just mdrun and I got this:
*~$ mdrun*
* *
* :-) G R O M A C S (-:*
*
*
*
Thanks Justin, I'm gonna take your advice.
On Thu, Feb 14, 2013 at 11:43 AM, Justin Lemkul jalem...@vt.edu wrote:
On 2/14/13 9:40 AM, David Sáez wrote:
Erik, thanks for your answer. I typed which mdrun and I got this output:
*~$ which mdrun*
*/usr/local/gromacs/bin/mdrun*
Then, I
Dear Justin,
I am not sure to follow you. You essentially say that it is better to avoid
using implicit solvent i.e. the generalized Born-formalism implemented in
GROMACS?
For the case of optimizing and relaxing a system (expecting short MD), I agree
that it might be preferable to use
On 2/14/13 10:21 AM, Sebastien Cote wrote:
Dear Justin,
I am not sure to follow you. You essentially say that it is better to avoid
using implicit solvent i.e. the generalized Born-formalism implemented in
GROMACS?
For the case of optimizing and relaxing a system (expecting short MD), I
Dear Justin,
Thank you very much for your answer.
I did not take this as a criticism of implicit solvent model. I was just
wondering what was the origin of the limitations you were speaking of.
I did some small implicit solvent simulations, but I must say that I have not
thoroughly looked at
On 2/14/13 11:02 AM, Sebastien Cote wrote:
Dear Justin,
Thank you very much for your answer.
I did not take this as a criticism of implicit solvent model. I was just
wondering what was the origin of the limitations you were speaking of.
I did some small implicit solvent simulations, but I
Hello Justin
Thank you very much for your effort and help. I will try adding new
parameter corresponding to the errors. Meanwhile just out of curiosity and
possible need, what should be done in case no matching parameters are
found for the missing dihedrals? I see that there are 6 fields in the
I have tried -pbc nojump, and other options given in that link but still my
protein gets jumped! Plz guide me, how to stop this ?
- orig.Message -
From : gmx-users-requ...@gromacs.org
To : gmx-users@gromacs.org
Sent date : 2013-02-14 18:42
Subject :
Hello Justin
Thank you very much for your effort and help. I will try adding new
parameter corresponding to the errors. Meanwhile just out of curiosity and
possible need, what should be done in case no matching parameters are
found for the missing dihedrals? I see that there are 6 fields in
On Mon, Feb 11, 2013 at 5:20 PM, Landraille
landry.charl...@univ-montp1.frwrote:
Last question (I hope).
How can I choose the force constant?
Indeed for the version 4.5, the force constant is defined by the
option dihre_fc in the mdp input file. After this force is multiply by
kfac
Please don't reply to the entire digest. Copy and paste relevant portions and
omit the rest.
On 2/14/13 11:54 AM, 라지브간디 wrote:
I have tried -pbc nojump, and other options given in that link but still my
protein gets jumped! Plz guide me, how to stop this ?
The suggested trjconv workflow
On 2/14/13 11:54 AM, Abhishek Acharya wrote:
Hello Justin
Thank you very much for your effort and help. I will try adding new
parameter corresponding to the errors. Meanwhile just out of curiosity and
possible need, what should be done in case no matching parameters are
found for the missing
On 2/14/13 4:15 PM, Abhishek Acharya wrote:
Hello Justin
Thank you very much for your effort and help. I will try adding new
parameter corresponding to the errors. Meanwhile just out of curiosity and
possible need, what should be done in case no matching parameters are
found for the missing
hi all,
i have done scattering function analysis using g_rdf command for
polymer-solvent system. i got the plot of scattering vector q(1/nm) vs
intensity .now i want to convert the scattering vector (q) value in to
distance i.e. 'd' the fundamental polymer books have the relation for light
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