Hello all:
I am a new GROMACS user. I am learning g_membrane in GROMCAS these
days.
It is said that the latest CHARMM36 with pre-equilibrium POPC performed
very well for membrane simulation and I try to use the POPC PDB file in
the website.
Hi all
I have inserted a new residue (DM instead of 5CM) and changed relative
files(dna.rtp,dna.r2b,dna.hdb,dna.arn ,residutypes.dat,defselection.dat),
but I have fatal erorrs in grompp:
{erorr1:[file epo0003-DNA-chain-A.itp ,line 2322]:
No default Angletypes}
{erorr2:[file
Hi Andrew,
looking at your protocol, perhaps I can help thermo- and barostating.
This are very important issues as they decide if your final trajectory
samples a canonical phase space that should correspond to the desired
ensemble( Tuckerman and Martyna, J. Phys. Chem. B 2000, 104, 159-178,
On 29/05/2011 7:29 PM, Masomeh Dehghani wrote:
Hi all
I have inserted a new residue (DM instead of 5CM) and changed relative
files(dna.rtp,dna.r2b,dna.hdb,dna.arn ,residutypes.dat,defselection.dat),
but I have fatal erorrs in grompp:
{erorr1:[file epo0003-DNA-chain-A.itp ,line 2322]:
No
Hi Kavya,
shortest periodic distance is 1.39714 (nm) at time 21824 (ps),
between atoms 2062 and 3688
where 2062 is a protein atom and 21824 is a water molecule.
21824 is the time in ps at which the two atoms indicated, 2062 and
3688, are at the short distance given. You can dump the frame
Hi all..
I want to ask if it is possible to restart the md run if due to power
problem final md run not completed means initiating md from where is stop
due to any reason?
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On 29 May 2011 14:45, rashi.pari...@gmail.com wrote:
Hi all..
I want to ask if it is possible to restart the md run if due to power
problem final md run not completed means initiating md from where is stop
due to any reason?
You can supply the checkpoint file written out, by -cpi option to
thanx sarath 4r reply..can u expalin little bit more..I did not get from
mdrun -h.
On , Sarath Chandra Dantu dsar...@gwdg.de wrote:
On 29 May 2011 14:45, rashi.pari...@gmail.com wrote:
Hi all..
I want to ask if it is possible to restart the md run if due to power
problem final md run
On 29/05/2011 10:45 PM, rashi.pari...@gmail.com wrote:
Hi all..
I want to ask if it is possible to restart the md run if due to power
problem final md run not completed means initiating md from where is
stop due to any reason?
Please use a meaningful subject line in emails. See
On May 29, 2011, at 20:45, rashi.pari...@gmail.com wrote:
Hi all..
I want to ask if it is possible to restart the md run if due to power problem
final md run not completed means initiating md from where is stop due to any
reason?
Suppose your .tpr is topol.tpr
mdrun -cpi state.cpt
Or
Dear Justin,
I used -res flag with the following command but I get pairs of values in the
output files. is there any mistake related with the command I used?
g_rmsf -s run.tpr -f run.xtc -o rmsf.xvg -od rmsdev.xvg -res
2011/5/29 jalem...@vt.edu
Quoting ahmet y?ld?r?m ahmedo...@gmail.com:
Hi,
I was running a replica exchange simulation in a PBS queue which was killed
as
my simulation crossed the maximum time limit. I was planning to restart the
simulation. I am using gromacs 4.0.7
I was wondering what should be the command line arguement for the multiple
.cpt file for
Dear all:
I would like to use charmm36 and POPC for membrane protein simulation. and I
am wondering where can I download charmm36 pre-pribriumed POPC PDB and topol
file for gromacs?
Thank you very much
Best
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gmx-users mailing listgmx-users@gromacs.org
You can build it using VMD (VIsual Molecular Dynamics)
2011/5/30 albert leu...@yeah.net
Dear all:
I would like to use charmm36 and POPC for membrane protein simulation.
and I am wondering where can I download charmm36 pre-pribriumed POPC PDB and
topol file for gromacs?
Thank you very
But I don't think it is pre-equilibrium POPC membrane.. and more over, the
position from VMD is not pre-aligned with OPM database. It would be a great
problem for putting our protein in the membrane..
At 2011-05-30，Sergio Manzetti sergio.manze...@vestforsk.no wrote:
You can build
Hello:
I am wondering, is it possible to convert NAMD topol psf file into Gromacs
topol format?
Thank you very much
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Il 29/05/2011 21:58, albert ha scritto:
Hello:
I am wondering, is it possible to convert NAMD topol psf file into
Gromacs topol format?
Thank you very much
Hi albert,
you can try with the following commands:
vmd .psf .pdb
topo writegmxtop output.top
I recently tried with vmd1.9
--
Dear users,
I am getting pairs of values in the output files as I said before. What is
this mean? Furthermore, though my system have 451 residue, it seems as 230
residue ( and 1th residue does not seem in the out files). What could be the
problem?
*
output file:*
# This file was created Sun May
Thank you very much for kind advices. Here is some warning, and I don't know
whether there would be some problem or not:
; 'fake' gromacs topology generated from topotools.
; WARNING| the purpose of this topology is to allow using the |WARNING
; WARNING| analysis tools from gromacs for non
Topology file is suitable for analysis. I succesfully used the .top to
analyse hydrogen bond and salt-bridges.
I don't know if problems would arise for simulation.
Il 29/05/2011 22:10, albert ha scritto:
Thank you very much for kind advices. Here is some warning, and I
don't know whether
Thank you very much for kind messages.
I am trying to convert a membrane system psf file for gromcas MD simulation.
For I would like to use CHARMM36 for my POPC system, but I cannot find
pre-equilibrium CAHRMM36 based POPC system. However, there is some for NAMD and
I download the pdf and psf
You can solve the problem without converting from namd to gromacs.
You can use the pdb you've already found to obtain a valid gromacs
topology through pdb2gmx
Il 29/05/2011 22:24, albert ha scritto:
Thank you very much for kind messages.
I am trying to convert a membrane system psf file for
Well, I also try to do this. But it seem that the atom name in my POPC pdb file
(which I download from here
http://terpconnect.umd.edu/~jbklauda/research/download.html ) is different from
the the one in Gromacs topol database. There are 72 lips in the system in all.
So, it would be very
I guess it is tedious but, in my opinion it is more correct changing the
atom name in the pdb and using gromacs topology generation tools. So you
are sure the topology will be suitable for gromacs simulation.
You rename atom, using the command sed.
In particular:
sed s/old/new/g file
Dear Gromacs users: I use gromacs.4-5-3 to calculate the free energy changes
for the GTG to GAG alchemy process, where charge annihilation is performed
first followed by soft core VDW calculation. When doing the soft core VDW
calculation, I see this error message ?Fatal error: [ file
Dear Sir/ Madam,
I would like to run simulation for water in
different water potentials like spc spc/e tip3p tip4p ... But when I do
pdb2gmx and genbox to solvate the box (l= 1.862) I am not able generate box
of 216 molecules. Please find me a solution.
Thank you in
Ravi Kumar Venkatraman wrote:
Dear Sir/ Madam,
I would like to run simulation for water in
different water potentials like spc spc/e tip3p tip4p ... But when I do
pdb2gmx and genbox to solvate the box (l= 1.862) I am not able generate
box of 216 molecules. Please
Hello sir,
I had used a dodecahedron cell for simulation. I have run
the simulation for 100ns, did you man I have to restart the
simulation again?
Thanking you
Kavya
On Sun, May 29, 2011 at 5:40 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Kavya,
shortest periodic distance is 1.39714
Hello Sir,
I saw the 21824th frame, it dint look unusually stretched when
I superposed against the initial pdb file. there atoms were hydrogen
atoms of two lysine residues.. And in the entire strttch of 100ns simulation
this is the only periodic image interaction observed, Is it possible to
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