Dear Mark,
Thank you very much for the quick reply to my post. According to your
suggestion, I check the table and reformat it with equal spacing between
entries. I also check the entries calculated from the analytical functions and
no wrong values are found. However, the same warnings are
Hi,
I recently got a nice Sun X6275 blade system
http://nf.nci.org.au/facilities/vayu/hardware.php (ok, not just for me!)
whose hardware ought to be better, but very comparable to that used in
the GROMACS 4 paper (http://pubs.acs.org/doi/abs/10.1021/ct700301q).
Figure 5 there demonstrates goo
wuxiao wrote:
> Dear GMXers,
>Recently, I has been performing coarse-grained MD simulations based
> on the tabulated potentials using GROMACS. In the initialization, some
> warnings are given as follows
> /WARNING: For the 999 non-zero entries for table 0 in table_b0.xvg the
> forces deviat
Dear GMXers,
Recently, I has been performing coarse-grained MD simulations based on the
tabulated potentials using GROMACS. In the initialization, some warnings are
given as follows
WARNING: For the 999 non-zero entries for table 0 in table_b0.xvg the forces
deviate on average 164% from m
Hi Par Bjelkmar,
I need to do an all atom simulation for dppc bilayer . You are right the
dppc molecule file that i have has PALM and PCGL residues.
I will like to try to set up the charmm FF for gromacs. But I dont have the
FF files with me, neither do i have the programs. Could you send me a
tu
Nancy wrote:
Hello,
I ran a docking simulation, and I have results in .mol format, and a
protein (.pdb format). I would like to save both as a single PDB file,
as input for Gromacs. Please advise as to what is the best way to do this.
Sounds like the sort of thing a *docking* program shoul
Nancy wrote:
Hello,
I ran a docking simulation, and I have results in .mol format, and a
protein (.pdb format). I would like to save both as a single PDB file,
as input for Gromacs. Please advise as to what is the best way to do this.
Try Open Babel:
http://openbabel.org/wiki/Main_Page
Hello,
I ran a docking simulation, and I have results in .mol format, and a protein
(.pdb format). I would like to save both as a single PDB file, as input for
Gromacs. Please advise as to what is the best way to do this.
Thanks,
Nancy
___
gmx-users
Hi,
I want to do some simulation about large fullerene balls. I searched the
website and searched the mailing list. The largest fullerene ball I can get
is C2160. But I want some larger ones like C3840 or so. Does anyone have any
information about the coordinates and topology of large fullerene ba
On Thu, 2009-10-15 at 21:04 +0200, Francesco Pietra wrote:
> $ lamboot
>
> $ mpirun.lam -np 4 mdrun_mpi.lam -s mod21.tpr -o minim_mod21_traj.trr
> -c minim_mod21.gro -e minim_mod21_ener.edr
clip
> Program mdrun_mpi.lam, VERSION 3.3.3
> Source code file: ../../../../src/mdlib/init.c, line: 69
>
On Thu, Oct 15, 2009 at 7:55 PM, Jussi Lehtola
wrote:
> On Thu, 2009-10-15 at 18:23 +0200, Francesco Pietra wrote:
>> Hi: I was trying to minimize in vacuum a pure CG protein on a four
>> core (two dual operons), getting errors:
>>
>> $ lamboot
>>
>> $ mpirun -np 4 mdrun -s mod21.tpr -o minim_mod2
Hi Diana,
> Well, minorities should not be disregarded just because they are poorly
> represented...In some cases a rare event makes all the difference. I think
> it would be helpeful to have the possiblity to calculate S-H...X bonds or
> X-H...S bonds with g_hbond.
In many cases these tools come
Diana Lousa
Protein Modelling Laboratory
Instituto de Tecnologia Química e Biológica
Universidade Nova de Lisboa
Portugal
On Thu, 15 Oct 2009, Justin A. Lemkul wrote:
Diana Lousa wrote:
Dear all,
Does any know why g_hbond does not (at least in a straightforward way)
enable the calculatio
On Thu, 2009-10-15 at 18:23 +0200, Francesco Pietra wrote:
> Hi: I was trying to minimize in vacuum a pure CG protein on a four
> core (two dual operons), getting errors:
>
> $ lamboot
>
> $ mpirun -np 4 mdrun -s mod21.tpr -o minim_mod21_traj.trr -c
> minim_mod21.gro -e minim_mod21_ener.edr
> ...
Hi: I was trying to minimize in vacuum a pure CG protein on a four
core (two dual operons), getting errors:
$ lamboot
$ mpirun -np 4 mdrun -s mod21.tpr -o minim_mod21_traj.trr -c
minim_mod21.gro -e minim_mod21_ener.edr
...
...
WARNING: Writing ompirun noticed that
Hi all,
I've got a question regarding freezing algorithm in
GROMACS. I appreciate it if somebody explains this.
I think in GROMACS 3 for freeze option to work it was
generally suggested that all the interactions inside the frozen part
should be excluded (either in top or mdp files). However it se
Hey,
the -ter in pdb2gmx worked with some additional modifications in the *.top -
file. I selected none for N- and C-terminus, so that no additional Hydrogens
were added. Then i manually added the bond between C (PGL) and N (PHE) and the
dihedral for this amide into the *.top - file.
Thanks a
rvers...@ccny.cuny.edu wrote:
Dear GROMACS users,
Does anyone know if there is some xdr library that allow to read .xtc
trajectories via perl? I'm trying to write a perl script to loop over .xtc
trajectories and so far I found only ways to read them in fortran.
No, but it ought to be straigh
Diana Lousa wrote:
Dear all,
Does any know why g_hbond does not (at least in a straightforward way)
enable the calculation of hbonds involving sulfur atoms (e.g. between
cysteines and other residues)? Is there an easy way to tell gromacs to
consider sulfur a donor and acceptor atom?
The p
Dear all,
Does any know why g_hbond does not (at least in a straightforward way)
enable the calculation of hbonds involving sulfur atoms (e.g. between
cysteines and other residues)? Is there an easy way to tell gromacs to
consider sulfur a donor and acceptor atom?
Thanks in advance
Diana Lousa
Dear GROMACS users,
Does anyone know if there is some xdr library that allow to read .xtc
trajectories via perl? I'm trying to write a perl script to loop over .xtc
trajectories and so far I found only ways to read them in fortran.
Thank you in advance for your help.
Rodney Versace
___
Pablo Englebienne wrote:
Hi all,
I have a question about the setting of improper dihedrals. I have a
pyrimidinone I want to use with the G53a5 force field, but I can't get
the ring to stay flat.
First question is: do all atoms in the planar ring need to have 3
subsituents? I.e., should an
Hi all,
I have a question about the setting of improper dihedrals. I have a
pyrimidinone I want to use with the G53a5 force field, but I can't get
the ring to stay flat.
First question is: do all atoms in the planar ring need to have 3
subsituents? I.e., should an explicit atom of type HC be
Tsjerk Wassenaar wrote:
Hey,
The problem comes from the special linkage between PGL and whatever the
subsequent amino acid is - the amide is formed through the side chain. As
such, you will need to specify a special bond in specbond.dat before this
connectivity will be recognized. If this i
Hey,
> The problem comes from the special linkage between PGL and whatever the
> subsequent amino acid is - the amide is formed through the side chain. As
> such, you will need to specify a special bond in specbond.dat before this
> connectivity will be recognized. If this is successful, then th
Christian wrote:
Justin Wrote:
Did you add PGL to aminoacids.dat?
Yes i added PGL to this file.
How did you specify your termini?
i'm not shure where i can define this - i only found such definitions in *rtp-
file?
Defining termini is done with pdb2gmx -ter, but as I think about it now
Justin Wrote:
> Did you add PGL to aminoacids.dat?
Yes i added PGL to this file.
> How did you specify your termini?
i'm not shure where i can define this - i only found such definitions in *rtp-
file?
the definitions there looks like this:
[ PGL ]
[ atoms ]
Nopls_238 -0.500 1
Nkwe Monama wrote:
Dear users,
I have never used gromacs. I'm trying to submit a gromacs job using
loadleveler. Below is the script I'm using:
**
# @ shell = /usr/bin/bash
# @ output = $(Executable).$(jobid).out
# @ error
Hi,
15 okt 2009 kl. 07.08 skrev gmx-users-requ...@gromacs.org:
The reason I am asking this is because it will require me to create
gromacs compatible FF files of the Charmm FF . I did find two perl
scripts which can do probably handle that but i am wondering if the
compatible FF are already up
haifeng yuan wrote:
Dear GROMACS users,
As a freshman in MD simulations, I am wondering whether it is
possible to carry out MD simulation of some specific peptides in
glycerol solvent. If possible, how to build the solvent box of glycerol
and solve the peptide into glycerol in GROMACS
Christian wrote:
Hello,
for my calculations i have to mutate the N-terminal Glutamate into an
Pyroglutamate (Pyroglutamic Acid). This modification was done with a modeling
program like chimera.
After this i changed the AS-name into PGLU (or PGL) and converted
the file again with editconf.
Dear GROMACS users,
As a freshman in MD simulations, I am wondering whether it is
possible to carry out MD simulation of some specific peptides in
glycerol solvent. If possible, how to build the solvent box of glycerol
and solve the peptide into glycerol in GROMACS ?
Thank you in
Hello,
for my calculations i have to mutate the N-terminal Glutamate into an
Pyroglutamate (Pyroglutamic Acid). This modification was done with a modeling
program like chimera.
After this i changed the AS-name into PGLU (or PGL) and converted
the file again with editconf.
This file i used to
Dear users,
I have never used gromacs. I'm trying to submit a gromacs job using
loadleveler. Below is the script I'm using:
**
# @ shell = /usr/bin/bash
# @ output = $(Executable).$(jobid).out
# @ error = $(Executable).$(job
ram bio wrote:
Dear Gromacs Users,
About Gromacs installation on the cluster, we compiled it on both the
login node and the computing nodes. I'd like to know which gromacs
programs can be run on the login node without disturbing all other
users and which ones must be run on the computing nodes (
Dear Gromacs Users,
About Gromacs installation on the cluster, we compiled it on both the
login node and the computing nodes. I'd like to know which gromacs
programs can be run on the login node without disturbing all other
users and which ones must be run on the computing nodes (e.g. the MD
progr
Hi,
Please file a bugzilla entry at bugzilla.gromacs.org
Include all the input files required to run grompp and mdrun.
Thanks,
Berk
From: lulany...@msn.com
To: gmx-users@gromacs.org
Date: Wed, 14 Oct 2009 15:25:02 -0400
Subject: [gmx-users] weird tabulated potential problem
Hi,
Some m
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