On 28/07/2012 4:49 PM, Rajitha Tatikonda wrote:
Hi,
I am intending to calculate binding affinity using Linear Interaction
method (LIE method) for which I need to perform two simulations for
given ligand both in free and bound states and get the values of
Electrostatic and Van der Waals Interacti
On 28/07/2012 3:01 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi,
my problem is, that during the md run the atoms are not frozen somehow.
During the minimization run everything worked out fine. But when I did a
md run the hydrogen atoms and the other atoms seems to be changes somehow
Dear Gromacs users!
Sometimes I need to calculate exact numbers of different molecules of
my system based on the initial gro file to add this information at the
end of the topol.top file. Its not trivial task for the big
heterogeneous systems ( e.g protein embeded into the membrane solvated
in wa
On 28/07/2012 6:23 PM, James Starlight wrote:
Dear Gromacs users!
Sometimes I need to calculate exact numbers of different molecules of
my system based on the initial gro file to add this information at the
end of the topol.top file. Its not trivial task for the big
heterogeneous systems ( e.g
hi gromacs users and especially Dr. Justine
in using the g_sgangle i have to define index file contain multiple of two
defining all the P and N atoms but after executing the g_sgangle i get the
message:something wrong with contents of index file
after defining the one p atom and 1 n atom then the
Thanks for your reply.
I'm following the protocol of Diagnosing an unstable system. Corresponding the
first step I changed th nstxout to 1 for 3 times.
The first and second time I got error the same as before ( some interactions
seem to be assigned multiple times ) and it the warning as below
I ran for the fourth time and got the error again. Now, I think the random
output of such a system is not reliable!
Sincerely,
Shima
- Original Message -
From: Shima Arasteh
To: Discussion list for GROMACS users
Cc:
Sent: Saturday, July 28, 2012 3:06 PM
Subject: Re: [gmx-users] s
Hi all,
My system has got BLOWING UP . I followed the protocol in
http://www.gromacs.org/Documentation/Terminology/Blowing_Up and got as below:
Step 1: If the crash is happening relatively early (within a few steps), set
nstxout (or nstxtcout) to 1, capturing all possible frames. Watch the
I think your RMSD of 0.000539742 is quite a small value, which can be,
at least theoretically, caused by the accumulation of errors. Can you
simulate your protein for a longer time to show that RMSD is indeed
significant?
On Sat, Jul 28, 2012 at 1:01 AM,
wrote:
> Hi,
> my problem is, that duri
On 7/28/12 7:34 AM, Shima Arasteh wrote:
Hi all,
My system has got BLOWING UP . I followed the protocol in
http://www.gromacs.org/Documentation/Terminology/Blowing_Up and got as below:
Step 1: If the crash is happening relatively early (within a few steps), set
nstxout (or nstxtcout) to
On 7/28/12 5:28 AM, yousef nademi wrote:
hi gromacs users and especially Dr. Justine
in using the g_sgangle i have to define index file contain multiple of two
defining all the P and N atoms but after executing the g_sgangle i get the
message:something wrong with contents of index file
after
I thought that the problem is with atom 18.
Allright, I'll go through the protocol again .
Thanks Justin.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Saturday, July 28, 2012 5:25 PM
Subject: Re: [gmx-u
Sorry, but when I don't get the outputs of mdrun , how is it possible to get
.xtc?
Any other command to get the trajectory?
Or you mean just viewing the nvt.gro in vmd?
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
us
Friends,
I have a completed simulation for 30ns (done with gro. 4.5.4), Now I
want to extend the simulation for another 30ns. In gromacs page (Ext.
simulations), I found the following procedure to extend the
simulations
tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr
On 29/07/2012 12:26 AM, Bala subramanian wrote:
Friends,
I have a completed simulation for 30ns (done with gro. 4.5.4), Now I
want to extend the simulation for another 30ns. In gromacs page (Ext.
simulations), I found the following procedure to extend the
simulations
tpbconv -s previous.tpr -e
On 28/07/2012 9:34 PM, Shima Arasteh wrote:
Hi all,
My system has got BLOWING UP . I followed the protocol in
http://www.gromacs.org/Documentation/Terminology/Blowing_Up and got as below:
Step 1: If the crash is happening relatively early (within a few steps), set
nstxout (or nstxtcout) to
> Thanks for your reply.
>
> I'm following the protocol of Diagnosing an unstable system. Corresponding
> the first step I changed th nstxout to 1 for 3 times.
> The first and second time I got error the same as before ( some interactions
> seem to be assigned multiple times ) and it the warning
On 29/07/2012 12:51 AM, Dr. Vitaly V. G. Chaban wrote:
Thanks for your reply.
I'm following the protocol of Diagnosing an unstable system. Corresponding the
first step I changed th nstxout to 1 for 3 times.
The first and second time I got error the same as before ( some interactions
seem to be
It's a little bit challenging problem I've got into! Certainly for me!
Thanks for your suggestions.
Sincerely,
Shima
- Original Message -
From: Mark Abraham
To: Discussion list for GROMACS users
Cc:
Sent: Saturday, July 28, 2012 7:15 PM
Subject: Re: [gmx-users] Diagnoding + system
It's a little bit challenging trouble I've got into! Of course for me.
Thanks for your suggestions.
Sincerely,
Shima
- Original Message -
From: Mark Abraham
To: Discussion list for GROMACS users
Cc:
Sent: Saturday, July 28, 2012 7:23 PM
Subject: Re: [gmx-users] Re: system blowing
Dear Mark, Thanks for your suggestions.
Atom 1 is the C which is expected to connect to the H ( atom 18) . Atom 5 is
tha CA of the next resisue ( Valine), the bond 18-5 is not expected at all!
However I see this pair in the [pairs] section of topology !
So I can get the result of an inappropria
Dear All,
The protein with which I'm working with, contains Zn metal and it
has tetrahedral coordination site. There are HISTIDINE side chains
within distance ~ 2.3 to 2.4 . So my questions are as follows
(1) In that distance range there is no possibility to form a covalent
bond between Zn and
Dear All ,
I wanted to keep all the molecules other than water fixed [
positiion restraints]. So for that I have performed short NVT
[simulation with DEPOSRE] after minimization, but while seeing the
movie of the trajectory in VMD I see the protein backbone is moving.
So did I miss somethi
Dear Mark, Thanks for your suggestions.
Atom 1 is the C which is expected to connect to the H ( atom 18) . Atom 5 is
tha CA of the next resisue ( Valine), the bond 18-5 is not expected at all!
However I see this pair in the [pairs] section of topology !
So I can get the result of an inappropri
On 7/28/12 2:47 PM, Shima Arasteh wrote:
Dear Mark, Thanks for your suggestions.
Atom 1 is the C which is expected to connect to the H ( atom 18) . Atom 5 is
tha CA of the next resisue ( Valine), the bond 18-5 is not expected at all!
However I see this pair in the [pairs] section of topolo
On 7/28/12 1:49 PM, tarak karmakar wrote:
Dear All ,
I wanted to keep all the molecules other than water fixed [
positiion restraints]. So for that I have performed short NVT
[simulation with DEPOSRE] after minimization, but while seeing the
movie of the trajectory in VMD I see the protei
On 7/28/12 1:43 PM, tarak karmakar wrote:
Dear All,
The protein with which I'm working with, contains Zn metal and it
has tetrahedral coordination site. There are HISTIDINE side chains
within distance ~ 2.3 to 2.4 . So my questions are as follows
(1) In that distance range there is no pos
Hello all,
I would like to add direction specific temperature coupling to the
nose-hoover thermostat. I am working with version 4.5.5. Basically the
idea would be not to include KE of one or more direction(s) to
calculate the temperature. I have looked at the file
$GMX_HOME/src/mdlib/coupling.c. C
Dear Users:
I would like to build a mixed lipid bilayer (POPE/POPG=3:1) in the MD using
Gromacs, please provide some tools for producing the structures or existing
structures (PDB or gro files).
Thank you very much!
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.or
On 29/07/2012 4:47 AM, Shima Arasteh wrote:
Dear Mark, Thanks for your suggestions.
Atom 1 is the C which is expected to connect to the H ( atom 18) . Atom 5 is
tha CA of the next resisue ( Valine), the bond 18-5 is not expected at all!
Uh-huh... there's a known initial issue with a bond bet
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