Hi Alex,
I read the manual but I got confused with the details. My pull_geometry =
position with pulling direction along y. I am trying to dissociate two
interacting proteins. So I set the last amino acid of one protein as my
reference group and the last amino acid of the other protein as the
Dear all,
I got an error while using pdb2gmx command (pdb2gmx -f 123.pdb -o
output.gro)
I used 13. GROMOS 53a6 force field
Fatal error:
Atom HA in residue GLU 1 was not found in rtp entry GLU with 12 atoms while
sorting atoms.
For a hydrogen, this can be a different protonation state, or it
hello sir
there was error in running grompp file of umbrella sampling... the error it
says
no such molecule type sol found...
how to debug the error
On Tue, Apr 23, 2013 at 3:30 PM, gmx-users-requ...@gromacs.org wrote:
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Hi Alex,
I read the manual but I got confused with the details. My pull_geometry =
position with pulling direction along y. I am trying to dissociate two
interacting proteins. So I set the last amino acid of one protein
We have noticed that g_genbox issue with MARTINI but have not new able to
understand where it actually comes from. It might be a bug or just a miss
communication of the vdw radius with genbox that appears only with large
spheres.
On Apr 29, 2013, at 19:50, alex.bjorling
I never looked into the code, but i understanded it the following way
(for pull_geometry = distane, direction, position).
For the pulling the reference group is held fixed and the force is
applied to the pulled group. Since the reference group an move during
the rest of the simulation (all
On 4/29/13 9:30 PM, maggin wrote:
Hi,
when I use GROMACS4.5.5 to do peptid simulation. At NVT step, system is not
equilibration, so I extend NVT simulation as follows:
tpbconv -s nvt.tpr -extend 2000 -o next1.tpr
mpirun -np 4 mdrun_mpi -reprod -s next1.tpr -cpi nvt.cpt
after finish this
On 4/30/13 2:59 AM, Nikunj Maheshwari wrote:
Dear all,
I got an error while using pdb2gmx command (pdb2gmx -f 123.pdb -o
output.gro)
I used 13. GROMOS 53a6 force field
Fatal error:
Atom HA in residue GLU 1 was not found in rtp entry GLU with 12 atoms while
sorting atoms.
For a hydrogen,
If you are starting a new topic, please give it an informative subject line and
do not reply to a digest message.
On 4/30/13 3:37 AM, Arunima Shilpi wrote:
hello sir
there was error in running grompp file of umbrella sampling... the error it
says
no such molecule type sol found...
how
Thanks Justin. I know that using -ignh will solve the problem. But I was
just curious because I got the same error message (Fatal error: Atom HD1
in residue HIS 65 was not found in rtp entry HISE with 17 atoms while
sorting atoms. ) when I used OPLS, this time it was His 65.
So I used -his option
On 4/30/13 6:10 AM, Nikunj Maheshwari wrote:
Thanks Justin. I know that using -ignh will solve the problem. But I was
just curious because I got the same error message (Fatal error: Atom HD1
in residue HIS 65 was not found in rtp entry HISE with 17 atoms while
sorting atoms. ) when I used
Dear All,
I'm fairly new to gromacs and having a bit of problem with the g_hydorder and
g_polystat. Thanks in advanced for your time.
For g_hydorder,
I get a fatal error when I type the following command:
g_hydorder_d -f file.gro -s file.tpr -n waters.ndx -o file1.xpm file2.xpm
Error:
Dear Gromacs users!
I have a question about umbrella sampling simulation based on the Justin's
tutorial.
According to the tutorial after definition of the set of conformers
extracted from the pulled trajectory I should run N equilibrating
simulations and N productions runs. In the tutorial I've
On 4/30/13 10:58 AM, James Starlight wrote:
Dear Gromacs users!
I have a question about umbrella sampling simulation based on the Justin's
tutorial.
According to the tutorial after definition of the set of conformers
extracted from the pulled trajectory I should run N equilibrating
On 4/30/13 6:24 AM, Emmanuel, Alaina wrote:
Dear All,
I'm fairly new to gromacs and having a bit of problem with the g_hydorder and
g_polystat. Thanks in advanced for your time.
For g_hydorder,
I get a fatal error when I type the following command:
g_hydorder_d -f file.gro -s file.tpr -n
I appologise, I meant defined at the same time without complaining, not just either direction.
Gesendet:Montag, 29. April 2013 um 22:23 Uhr
Von:lloyd riggs lloyd.ri...@gmx.ch
An:S. Watkins gmx-users@gromacs.org
Betreff:Aw: [gmx-users] Re: how is the pulling force measured
Dear All,
Doing a
Justin,
could you also tell me
1) what difference should be expected from the umbrella sampling run with
(as I want to do for better coverage) and without (as in your tutorial)
velocities re-assignment on each umbrella window run ?
2) On what suggestions should I chose each conformer from
Hi
I am following the git tutorial for the novice. It says to check out stable
version
one should use git checkout --track -b release-4-5-patches
origin/release-4-5-patches
Is there stable branch for 4.6? If yes, how do get it? I tried replacing
4-5 by 4-6 but I get the error:
fatal: git
On 4/30/13 12:33 PM, lloyd riggs wrote:
I appologise, I meant defined at the same time without complaining, not just
either direction.
A different atom order is interpreted as a different interaction. In this case,
if both are defined, there is indeed a difference in the improper energy
On 4/30/13 1:38 PM, James Starlight wrote:
Justin,
could you also tell me
1) what difference should be expected from the umbrella sampling run with
(as I want to do for better coverage) and without (as in your tutorial)
velocities re-assignment on each umbrella window run ?
You have to
On 4/30/13 3:03 PM, Sikandar Mashayak wrote:
Hi
I am following the git tutorial for the novice. It says to check out stable
version
one should use git checkout --track -b release-4-5-patches
origin/release-4-5-patches
Is there stable branch for 4.6? If yes, how do get it? I tried replacing
hi, Justin,
Thank you very much! Thank you!
Ya, it's works! great! cool!
Thank you very much for your suggestion, this time I also not use -reprod
,it doesn't effect simulation. Work also can go on!
Thank you very much for your kind help!
maggin
--
View this message in context:
Hi
I have set up two small systems, one with a single POPC lipid, and another
system with 23 POPC's arranged as a lipid bilayer. I am hoping to do a
similar comparison as in Table 1 in the Par Bjelkmar et al paper (porting
charmm ff to gromacs) for my systems. My main question is that for the
Hi
I found the branch of gromacs code called localpressure-4.0 at
http://redmine.gromacs.org/projects/gromacs/repository/show?rev=localpressure-4-0.
I am wondering whether this code can compute the spatial variation of
pressure in given system. And if it does, how stable is this branch? Are
there
Thanks Justin.
I replaced release-4-5-patches with release-4-6 while checking out the
branch.
When I installed it and checked the version string I get VERSION
4.6.2-dev-20130429-d13fc48.
Does that mean I got the version which is still under development and not
stable and tested?
Should I be
On 4/30/13 4:19 PM, Reza Salari wrote:
Hi
I have set up two small systems, one with a single POPC lipid, and another
system with 23 POPC's arranged as a lipid bilayer. I am hoping to do a
similar comparison as in Table 1 in the Par Bjelkmar et al paper (porting
charmm ff to gromacs) for my
On 4/30/13 8:01 PM, Sikandar Mashayak wrote:
Hi
I found the branch of gromacs code called localpressure-4.0 at
http://redmine.gromacs.org/projects/gromacs/repository/show?rev=localpressure-4-0.
I am wondering whether this code can compute the spatial variation of
pressure in given system. And
On 4/30/13 8:28 PM, Sikandar Mashayak wrote:
Thanks Justin.
I replaced release-4-5-patches with release-4-6 while checking out the
branch.
When I installed it and checked the version string I get VERSION
4.6.2-dev-20130429-d13fc48.
Does that mean I got the version which is still under
Hi Justin
Thanks for explanation. But I am a bit confused because I am new to git.
When I check out release-4-6 branch, the source code should be the same as
the one in tarball from Gromacs website, right? When I run git status I get
# On branch release-4-6
nothing to commit (working directory
On 4/30/13 8:50 PM, Sikandar Mashayak wrote:
Hi Justin
Thanks for explanation. But I am a bit confused because I am new to git.
When I check out release-4-6 branch, the source code should be the same as
the one in tarball from Gromacs website, right? When I run git status I get
# On branch
Hello Justin,
My mdp file shows that the pbc was set to xyz.
Kind Regards,
Alaina
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin Lemkul [jalem...@vt.edu]
Sent: 30 April 2013 16:10
To: Discussion list for
Hello Justin,
My mdp file shows that the pbc was set to xyz.
Kind Regards,
Alaina
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin Lemkul [jalem...@vt.edu]
Sent: 30 April 2013 16:10
To: Discussion list for
Sir
My query is how to generate input file for umbrella sampling???
On Wed, May 1, 2013 at 6:34 AM, gmx-users-requ...@gromacs.org wrote:
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Message: 5
Date: Tue, 30 Apr 2013 21:38:17 +0400
From: James Starlight jmsstarli...@gmail.com
Subject: Re: [gmx-users] Umbrella sampling's equilibration runs
To: Discussion list for GROMACS users gmx
Sir,
I studying the dynamics of a peptide in explicit solvent model.But
during the mdrun I got the message like this.
NOTE 1 [file md.mdp]:
This run will generate roughly 1177130 Mb of data
why the run generating this much amount of data?
The md.mdp file I used is shown below
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