Dear All,
I am studying a molecule which is changing its conformation
during a reaction. So I want to calculate free energy for the
conformational change. I am planning to do Umbrella sampling for this
purpose. But what is the way to handle the dihedral angle as a
Collective Variable (C
On 2012-08-09 12:34:19PM -0300, Sebastien Cote wrote:
>
> Dear Peter,
>
> Did you use any different simulation conditions for your POPC membrane? I
> tried many different ones for POPE, without never reproducing Klauda's
> results. I may try yours on my POPE membrane.
I used vdwswitch of 0.8
hello justin,
I got one more error, please help me out again.
I got the em.gro instead of confout.gro. I reached an area per lipid of ~52 Å2
for POPE bi layer.
Next i tried to add ions to the system after solvating with water. i get the
following error.
Program grompp, VERSION 4.5.4
Source code
Hi Mark,
Thanks for your reply. I will try to follow your instructions.
Thanks,
Jesmin
On Thu, Aug 9, 2012 at 9:06 PM, Mark Abraham wrote:
> On 10/08/2012 3:06 AM, jesmin jahan wrote:
>>
>> Dear Gromacs Users,
>>
>> I am a new user of Gromacs and I am using gromacs to calculate
>> GB-polarizat
On 10/08/2012 3:06 AM, jesmin jahan wrote:
Dear Gromacs Users,
I am a new user of Gromacs and I am using gromacs to calculate
GB-polarization energy .
I have a couple of questions about it. It would be great if someone
can answer them. Thanks in advance.
Questions:
1: I got an output like th
On 8/9/12 7:02 PM, Paula Andrea Delgado Pinzon wrote:
Good afternoon, I run a molecular dynamics simulation of two protein complex
with periodic boundaries, when i check the trajectory file i realized that
the molecules were split so i decided to use the trjconv command with the
option -pbc, i
Good afternoon,
I run a molecular dynamics simulation of two protein complex with periodic
boundaries, when i check the trajectory file i realized that the molecules were
split so i decided to use the trjconv command with the option -pbc, i tried
with -pbc atom, -pbc res and they didn't seem to
Hi Jose,
I will start by telling you that I do not have an exact answer for your
problem since I did not encounter this particular problem myself. However,
your are reply-less for 3 days already so better a crazy idea than no idea.
Anyhow, if I am totally wrong, my reply would at least generate so
On 8/9/12 2:32 PM, Shima Arasteh wrote:
OK, I got it. But how can I get a .xtc output of NPT or NVT equilibration? The
output of mdrun -deffnm npt doesn't have any .xtc files to visualize by VMD. I
have seen that I get .xtc file just after the final mdrun -deffnm md (as you
said).
An .xt
OK, I got it. But how can I get a .xtc output of NPT or NVT equilibration? The
output of mdrun -deffnm npt doesn't have any .xtc files to visualize by VMD. I
have seen that I get .xtc file just after the final mdrun -deffnm md (as you
said).
Sincerely,
Shima
- Original Message -
Fr
You mean I can not see the NPT equilibration process!
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Thursday, August 9, 2012 10:45 PM
Subject: Re: [gmx-users] Visualizing a process
On 8/9/12 2:12 PM, S
On 8/9/12 2:21 PM, Shima Arasteh wrote:
You mean I can not see the NPT equilibration process!
I mean exactly what I said. You can load the .xtc file as data for a coordinate
file in, e.g. VMD, and watch the movie of the simulation after it is complete.
-Justin
Sincerely,
Shima
-
On 8/9/12 2:12 PM, Shima Arasteh wrote:
Hi,
Is it possible to view the process of a NPT or NVT equilibration? Which command
in gromacs can generate a .xtc output?
Only mdrun writes .xtc files of simulations. As far as I know, one cannot watch
the simulation in real time but .xtc files ca
Hi,
Is it possible to view the process of a NPT or NVT equilibration? Which command
in gromacs can generate a .xtc output?
Thanks in advance.
Sincerely,
Shima
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Dear All,
I am studying a molecule which is changing its conformation
during a reaction. So I want to calculate free energy for the
conformational change. I am planning to do Umbrella sampling for this
purpose. But what is the way to handle the dihedral angle as a
Collective Variable (C
On 8/9/12 1:40 PM, Shima Arasteh wrote:
Dear gmx users,
Would be this error (as you see here) a symptom of blowing up of a system? Or
just .mdp options should be changed?
Fatal error:
1 of the 16625 bonded interactions could not be calculated because some atoms
involved moved further apart
Dear gmx users,
Would be this error (as you see here) a symptom of blowing up of a system? Or
just .mdp options should be changed?
Fatal error:
1 of the 16625 bonded interactions could not be calculated because some atoms
involved moved further apart than the multi-body cut-off distance (0.8176
Dear Gromacs Users,
I am a new user of Gromacs and I am using gromacs to calculate
GB-polarization energy .
I have a couple of questions about it. It would be great if someone
can answer them. Thanks in advance.
Questions:
1: I got an output like this in log file from a protein simulation:
R
Dear Peter,
Did you use any different simulation conditions for your POPC membrane? I tried
many different ones for POPE, without never reproducing Klauda's results. I may
try yours on my POPE membrane.
In my simulations, I want to study peptide-membrane interactions. The peptide
is not emb
Hi Justin,
Thank you so much for a swift response. I will try as suggested and
get back to you with my hurdles.
Appreciate the help!
Best Wishes,
Ankita
On Thu, Aug 9, 2012 at 4:09 PM, Justin Lemkul wrote:
>
>
> On 8/9/12 10:40 AM, Ankita naithani wrote:
>>
>> Hi all,
>>
>> I am trying to put
On 8/9/12 10:40 AM, Ankita naithani wrote:
Hi all,
I am trying to put a tetrameric protein for Energy Minimization to be
followed by MD simulation of course. But, my problem is that it is a
tetramer and also I need to perform the simulation with the ligand. I
have read the tutorial for Protein
Hi all,
I am trying to put a tetrameric protein for Energy Minimization to be
followed by MD simulation of course. But, my problem is that it is a
tetramer and also I need to perform the simulation with the ligand. I
have read the tutorial for Protein-Ligand simulation but that explains
for only o
On 2012-08-09 05:56:46AM -0700, Shima Arasteh wrote:
> Thanks for replies.
>
> Some bonds are rotated more than 30 degrees ,as it's written just before
> turning off the equilibration.
> Is this over-rotation also included in interaction with PBC images?
So the system crashed before LINCS did. P
Thanks for replies.
Some bonds are rotated more than 30 degrees ,as it's written just before
turning off the equilibration.
Is this over-rotation also included in interaction with PBC images?
Am I supposed to change the rcoulomb and rvdw cutoffs? How would I be sure of a
correct changes?
Sin
Parts of your system shifted too much (in Y dimension) for PME to handle.
What happens to the system up to the point of the crash?
How large is the system (particle count) vs. # of PME nodes used?
Could be your system is too small for the # of PME nodes used
Is the protein somehow interacting wi
Are you running NVT with position restraint dynamics of your protein?
Your system is probably not minimizied enough.
Jan
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Shima Arasteh [shima_arasteh2...@yahoo.com]
Sent: Thu
Dear gmx users,
I used the NVT (T=300) equilibration for my system ( a protein in water). The
first time, I set 100 ps for system for equilibration, It resulted in RMSD=3.96
with an average temperature around 299.803 K.
Then I though of a better convergence, so set the equilibration to 200 ps.
On 8/9/12 6:31 AM, sai nitin wrote:
Hi justin,
Yes swiss param gave me ligand.itp file which gromacs topologies i
included in topol.top file which i generated ..usign PDB2GMX so no
need of creating seperate topol.top file for ligand only? can i use
same topol.top file to run MD to simulate onl
Hi justin,
Yes swiss param gave me ligand.itp file which gromacs topologies i
included in topol.top file which i generated ..usign PDB2GMX so no
need of creating seperate topol.top file for ligand only? can i use
same topol.top file to run MD to simulate only ligand because current
topol.top file
Dear Gmx Users,
I have on the HPC cluster installed Gromacs VERSION
4.6-GPU-dev-20120607-7ce3372 (called gromacs 4.6-hybrid-beta). I want
to simulate chain of 80 residues in explicit solvent model using GPUs.
Has anyone simulated the system like this under this version and can
advise about mdp o
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