Hi,
I am implementing some addition stuff to mdrun, but my mdrun (in
particle decomposition) stops with lincs warings after running fine for
10 to 50 ps or so. The same system with the git master does not crash
(with -pd), which, of course, does not mean there is no memory leak as
well. So I
Dear users,
I'm simulating a box of cyclohexane (GROMOS 53a6, 512 molecules, 298K,
compressibility=11.2 10-5 bar-,1 tau_p=0.5 ps, no constraints on bonds).
After equilibration and NPT simulation, the system reaches the proper
density reported for the model (791g/L). When I switch to a
Hi,
First of all, Gromacs is full of memory leaks, which by itself it not so nice,
but this is not a problem (unless we are eating up all the memory).
I guess you meant to say illegal memory access iso memory leaks.
The current valgrind warnings in the graph code are due to a bug in valgrind.
Hi,
I have a problem with Gromacs. I want to do MD simulations with my proteïn in a
DPPC-membrane.
Therefore I followed Justin Lemkul's tutorial on membrane proteïn simulation. I
just used a bigger
membrane (256 lipids instead of 128). I managed to correctly embed the proteïn
in the
Dear Gromacs Developers,
I'm intested in a workshop for Gromacs. Is there a workshop planned in 2010 ?
Kind Regards,
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Hi,
please see: http://tfy.tkk.fi/soft/levi2010/
Rasoul
On Thu, Jan 28, 2010 at 12:42 PM, oguz gurbulak gurbulako...@yahoo.comwrote:
Dear Gromacs Developers,
I'm intested in a workshop for Gromacs. Is there a workshop planned in
2010 ?
Kind Regards,
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Hi Marysa,
The error is about the definition of mulecules, which suggests that
there are no [ moleculetype ] directives. Did you #include the proper
.itp file(s) with the necessary moleculetype definitions? If not,
you'll have to provide more information, probably posting the topology
file
Do you have the right number of atoms indicated on the second line of the .gro
file? What is in your [molecules] directive in your topology?
-Justin
Marysa van den Berg wrote:
Hi,
I have a problem with Gromacs. I want to do MD simulations with my
proteïn in a DPPC-membrane.
Therefore I
I have to recreate .gro file from .trr file by using trjconv which i
have deleated previously for disk space reasons , im using following
commond for that
trjconv -f full.trr -s full.tpr -o fullout.gro .
so my question is will this commond give me the same gro file that it
Please use a descriptive subject line. Simply using Hi will often not attract
the attention of someone who can help you, and other times will get trapped in a
spam filter, depending on the settings of the server or email client.
pavan payghan wrote:
I have to recreate .gro file from
Hi,
I tried to run the command
mdrun -deffnm em
on cluster,
blow is the script, but I worried that it might be some place wrong, seems no
files came out after several hours running
Is anyone please help me to modify it, and how can know the process of its
running in the cluster.
Thanks and
Hi,
would you please elaborate the first column in the hblife.xvg file?
hblife.xyg is the output of the following command:
g_hbond -life hblife.xvg
this column don't show the real time in simulated system.what are these
times?
thanks in advance,
Afsaneh
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afsaneh maleki wrote:
Hi,
would you please elaborate the first column in the hblife.xvg file?
hblife.xyg is the output of the following command:
g_hbond -life hblife.xvg
this column don't show the real time in simulated system.what are these
times?
Check the headers in the .xvg file;
Dear Aymeric:
1. Can we please see the entire .mdp files for both simulations? I
suggest that you use a tau_t=1.0 (0.2 is probably over-damped).
2. Although any value of tau_t should still produce the correct
equilibria, your diffusion rates and your overall sampling may be
slower with
thanks dear justin'
it is right that the output of the analysis tools generally writes axis
labels and data set legends. in hblife.xyg file is written that x axis
label Time (ps) and the last time is written 14300.001 whereas my
simulated time is 4 ps not 143000.00 ps
i send you this file
- Original Message -
From: #ZHAO LINA# zhao0...@ntu.edu.sg
Date: Friday, January 29, 2010 1:11
Subject: [gmx-users] mpi_run issue
To: gmx-users@gromacs.org
Hi,
I tried to run the command
mdrun -deffnm em
on cluster,
blow is the script, but I worried that it might be some place
afsaneh maleki skrev:
thanks dear justin'
it is right that the output of the analysis tools generally writes
axis labels and data set legends. in hblife.xyg file is written that
x axis label Time (ps) and the last time is written 14300.001
whereas my simulated time is 4 ps not
- Original Message -
From: afsaneh maleki maleki.afsa...@gmail.com
Date: Friday, January 29, 2010 1:56
Subject: Re: [gmx-users] hblife
To: jalem...@vt.edu, Discussion list for GROMACS users gmx-users@gromacs.org
thanks dear justin'
it is right that the output of the analysis tools
- Original Message -
From: Mark Abraham mark.abra...@anu.edu.au
Date: Friday, January 29, 2010 2:16
Subject: Re: [gmx-users] hblife
To: Discussion list for GROMACS users gmx-users@gromacs.org
- Original Message -
From: afsaneh maleki maleki.afsa...@gmail.com
Date: Friday,
Hi,
Here is the example file I based on to modify,
mpi.sh
#!/bin/bash
#
## Specify the job name
#PBS -N jobname
## Join the standard error and the standard output into 1 file output
#PBS -j oe
#PBS -V
## To run on 16 cpus
#PBS -l nodes=2:ppn=8
## pre-processing script
cd $PBS_O_WORKDIR
Hello,
I am attempting to construct the free energy profile for rotation of a
short peptide hairpin. For this purpose, I am using [
angle_restraints_z ]. I will focus this post on the simplified test
system that I have been using to characterize the problem that I am
experiencing: single
Hello everyone,
I use the g_order to get the order parameter of the tails( C1A, C2A, C3A,
C4A) of DPPC. The are 100 molecules of DPPC
1. I use the make_ndx -f dppc.trr -n index to produce the index file.
a C1A
a C2A
a C3A
a C4A
del 0-3
Q_1: Is the method right to produce the index file?
lammps lammps wrote:
Hello everyone,
I use the g_order to get the order parameter of the tails( C1A, C2A,
C3A, C4A) of DPPC. The are 100 molecules of DPPC
1. I use the make_ndx -f dppc.trr -n index to produce the index file.
a C1A
a C2A
a C3A
a C4A
del 0-3
Q_1: Is the method
Hi,
I was trying to figure out if there is a short-cut for what I'm doing. I
have complexes that I'm trying to prep using pdb2gmx. The ligand does not
have a standard residue name. The way I know this can work is seperating out
the ligand and protein into seperate files and preping the ligand
Hi everybody
I am currently testing the CHARMM port for GROMACS pre4.1. I have downloaded
the c32b1_release_1.1.zip file http://www.dbb.su.se/User:Bjelkmar/Ffcharmm
(11:59, 23 Oct 2009). My protein protein have an acetylated N-terminus and
amidated C-terminus. According to the CHARMM force
Hi,
The number of atoms in the second line of my .gro file are correct, I checked
that.
This is what my topology file says in the beginning:
[ moleculetype ]
; Name nrexcl
Protein 3
No changes here after the solvation.
At the end after the [ atoms ] directive:
Marysa van den Berg wrote:
Hi,
The number of atoms in the second line of my .gro file are correct, I
checked that.
This is what my topology file says in the beginning:
[ moleculetype ]
; Name nrexcl
Protein 3
No changes here after the solvation.
At the end after the [
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- Original Message -
From: Jack Shultz j...@drugdiscoveryathome.com
Date: Friday, January 29, 2010 4:15
Subject: [gmx-users] including a custom itp file in topology
To: Discussion list for GROMACS users gmx-users@gromacs.org
Cc: Alan alanwil...@gmail.com, Andrey Voronkov
Hi, while perform simulation, I perceive nether warning , I recourse
page 87147manual (PME part ),but I can 't understand that how apply
change in the .mdp file according to said direction in the nether
warning . please guide me, how remove error. consist warning :
Can not exclude the lattice
On 29/01/10 14:54, neo lotus wrote:
Hi, while perform simulation, I perceive nether warning , I recourse
page 87147manual (PME part ),but I can 't understand that how apply
change in the .mdp file according to said direction in the nether
warning . please guide me, how remove error. consist
Hi,
I wanted to inquire about the vacuum FF distributed officially with
GROMACS-4.0.5. I wish to carry out a vacuum MD of ~300 aa protein
FF.dat file mentions of G43b1 as officially distributed vacuum FF. But there
are no FF related files-.rtp,.hdb etc present. Is that the case that GROMACS-4
Hi,
I removed this force field on purpose.
The name is already very confusing. It is not a vacuum force field at all.
It is an implicit solvent force field, but a quite bad one.
It only scales down the charges on groups with net charge.
If you really want to simulate a protein in vacuum do NOT
On 1/29/10 8:29 AM, Berk Hess wrote:
Hi,
I removed this force field on purpose.
The name is already very confusing. It is not a vacuum force field at all.
It is an implicit solvent force field, but a quite bad one.
It only scales down the charges on groups with net charge.
If you really want to
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