Dear Sir,
Thanks for your reply. I will check it..
On Tue, Dec 6, 2011 at 12:26 PM, Justin A. Lemkul wrote:
>
>
> Sathish wrote:
>
>>
>> Dear all,
>>
>> How to run simulation in different PH?
>>
>> Kindly help to fix this problem. Thanks in advance...
>>
>>
> The concept of "pH" is ill-defined
Please check the paper by Grigera JCP 2001 114 8064 for the derivation
for this model.
[ moleculetype ]
; molname nrexcl
SOL 2
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 OD 1SOL OW 1 -0.8715.99940
2
Message: 3
Date: Tue, 06 Dec 2011 18:58:50 +0100
From: Javier Cerezo
Subject: Re: [gmx-users] RE: logfile size
To: Discussion list for GROMACS users
Message-ID: <4ede57da.80...@um.es>
Content-Type: text/plain; charset=UTF-8; format=flowed
Not the main problem, but your dt=0.0002 (0.2fs), is it
You mean that
$> ls /home/fftw
gives you the content of the installed fftw library (i.e. bin/
include/ lib/ share/)?
El 06/12/11 16:21, aiswarya.pa...@gmail.com escribió:
Hi,
Thanks for the reply, I check the path and everything still I get this error.
Sent from my BlackBerry® on Relia
On 7/12/2011 7:41 PM, lloyd riggs wrote:
Message: 3
Date: Tue, 06 Dec 2011 18:58:50 +0100
From: Javier Cerezo
Subject: Re: [gmx-users] RE: logfile size
To: Discussion list for GROMACS users
Message-ID:<4ede57da.80...@um.es>
Content-Type: text/plain; charset=UTF-8; format=flowed
Not the main prob
when i gave following command for gromacs=
./configure --with-fft=fftw3 --enable-float --disable-threads
it installed gromacs successfully, but i require a mpi mdrun. when i give
enable mpi it gives me same error as fftw3 library not found.
Thanks
On Wed, Dec 7, 2011 at 2:21 PM, Javier Cerezo
On 7/12/2011 11:25 PM, aiswarya pawar wrote:
when i gave following command for gromacs=
./configure --with-fft=fftw3 --enable-float --disable-threads
it installed gromacs successfully, but i require a mpi mdrun. when i
give enable mpi it gives me same error as fftw3 library not found.
Proba
Dear All,
I am trying to simulate the ethylacetate in OPLSAA forcefield.
The parameters for the ethylacetate is already there in OPSSAA.ff
directory. But when I give links for the Improper Dihedral it shows error
like "no default dihedral type". How to include the improper dihedral
par
Ravi Kumar Venkatraman wrote:
Dear All,
I am trying to simulate the ethylacetate in OPLSAA
forcefield. The parameters for the ethylacetate is already there in
OPSSAA.ff directory. But when I give links for the Improper Dihedral it
shows error like "no default dihedral type". How
Original-Nachricht
> Datum: Wed, 7 Dec 2011 12:00:05 +0100 (CET)
> Von: gmx-users-requ...@gromacs.org
> An: gmx-users@gromacs.org
> Betreff: gmx-users Digest, Vol 92, Issue 34
> Send gmx-users mailing list submissions to
> gmx-users@gromacs.org
>
> To subscribe or unsubs
Dear All,
I had been running Gromacs 4.0.7 on a 12-node cluster (Intel i7-920
4-cores) with OS Rocks 5.4.2. Recently, I have upgraded the cluster OS
to Rocks 5.4.3 and I have installed Gromacs 4.5.4 from the Bio Roll
repository. When running in parallel on the same node, everything works
fine. How
On 8/12/2011 1:26 AM, Nikos Papadimitriou wrote:
Dear All,
I had been running Gromacs 4.0.7 on a 12-node cluster (Intel i7-920
4-cores) with OS Rocks 5.4.2. Recently, I have upgraded the cluster OS
to Rocks 5.4.3 and I have installed Gromacs 4.5.4 from the Bio Roll
repository. When running in
Dear Gromacs users,
I'm new to gromacs. I want to simulate a short peptide in an implicit
solvent with low dielectric constant (simulate the interior of a membrane).
Can you please tell me which implicit solvent force field is more suitable,
and how do I pass the value of the dielectric constant ?
Dear Gromacs users,
Im new to gromacs and I'm following a tutorial (
http://nmr.chem.uu.nl/~tsjerk/course/molmod/). Unfortunately, the tutorials
doesn't say anything about how to update the topology file after using
'genion' to replace a few water molecules with ions.
I manually edited the topolog
Jose Borreguero wrote:
Dear Gromacs users,
Im new to gromacs and I'm following a tutorial
(http://nmr.chem.uu.nl/~tsjerk/course/molmod/). Unfortunately, the
tutorials doesn't say anything about how to update the topology file
after using 'genion' to replace a few water molecules with ions.
Hi Justin, thanks for your reply!
I appended '-p protein.top' to genion. File protein.top was automatically
updated by insertion of the following lines at the end of the file:
*[ molecules ]
; Compound#mols
Protein_chain_A 1
SOL 7791
NA+ 26
CL- 23*
My solvated
Dear gmx_users,
I am using gmx_4.0.7. I need to print the box vectors from the trajectory
of a simulated system. How can this be achieved? Can someone help me out?
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mai
Dear gmx_users,
I was just wondering how the g_msd (of gmx 4.0.7) code, takes care of the
PBC. e.g. If I want to calculate the lateral diffusion of a lipid bilayer
and at some point of the trajectory, some lipid molecules, due to PBC in
the lateral direction, might pop out from one side of the box
Hi everyone. I'm doing a simulation in gromacs using the charmm36 parameters
from the gromacs website. The parameters don't seem to have carbohydrates,
which are part of the charmm36 force field. In particular, I need parameters
for trehalose. Is there anywhere I can find these parameters in a
Jose Borreguero wrote:
Hi Justin, thanks for your reply!
I appended '-p protein.top' to genion. File protein.top was
automatically updated by insertion of the following lines at the end of
the file:
/[ molecules ]
; Compound#mols
Protein_chain_A 1
SOL 7791
NA+ 26
Chandan Choudhury wrote:
Dear gmx_users,
I am using gmx_4.0.7. I need to print the box vectors from the
trajectory of a simulated system. How can this be achieved? Can someone
help me out?
Box vectors are stored in the .edr file.
-Justin
--
Ju
#!/usr/bin/env python
# Python compliant email -- Just save the content :)
"""
Hey :)
The neatest way is using python to extract them from the XTC file :)
"""
from struct import unpack
import sys
import os
def i(x): return sum([ord(x[j])<<(24-j*8) for j in range(4)])
def strseek(stream,s
Hi Chandan,
Pretty simple; you just take the smallest distance between the time
points in the periodic system.
Cheers,
Tsjerk
On Wed, Dec 7, 2011 at 6:44 PM, Chandan Choudhury wrote:
>
> Dear gmx_users,
>
> I was just wondering how the g_msd (of gmx 4.0.7) code, takes care of the
> PBC. e.g. I
All of the Charmm force field parameters may be found on Alex
MacKerell's website: http://mackerell.umaryland.edu/
CHARMM_ff_params.html. Converting from Charmm units and potential
form to Gromacs is straightforward.
Andrew
On Dec 7, 2011, at 12:59 PM, Michael McGovern wrote:
Hi everyone.
Impressive :)
On Wed, Dec 7, 2011 at 1:34 PM, Tsjerk Wassenaar wrote:
> #!/usr/bin/env python
>
> # Python compliant email -- Just save the content :)
>
>
> """
>
> Hey :)
>
> The neatest way is using python to extract them from the XTC file :)
>
> """
>
> from struct import unpack
> import sys
Hi All,
Is there any way of calculating RMSD of only a certain portion of
protein structure after simulation. Like in Amber ptraj utility has this
option to mask out certain portion in RMSD.
Thanks
Rohit
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/list
Rohit Farmer wrote:
Hi All,
Is there any way of calculating RMSD of only a certain portion of
protein structure after simulation. Like in Amber ptraj utility has this
option to mask out certain portion in RMSD.
Yes, use an index group containing the residues/atoms of interest.
-Justin
This tutorial doesn't seem to be quite useful, if so many errors pop up.
Maybe it was implemented for Gromacs < 4.5.x but there's no info on the
version it should be used.
However, Lo and behold! I found that you have a nice page with Gromacs
4.5.x tutorials :D (
http://www.bevanlab.biochem.vt.ed
Hi,
I encounter the following error when trying to execute mdrun:
# Running Gromacs: read TPR and write output to /gpfs disk
$MPIRUN $MDRUN -v -nice 0 -np $NSLOTS \
-s n12_random_50_protein_all.tpr \
-o n12_random_50_protein_all.trr \
-c n12_random_50_protein_all.gro \
-g n12_random_50_prot
On 8/12/2011 4:36 AM, Chandan Choudhury wrote:
Dear gmx_users,
I am using gmx_4.0.7. I need to print the box vectors from the
trajectory of a simulated system. How can this be achieved? Can
someone help me out?
g_energy on the .edr file (assuming that the vectors actually vary).
Mark
--
gm
On 8/12/2011 7:36 AM, rainy908 wrote:
Hi,
I encounter the following error when trying to execute mdrun:
# Running Gromacs: read TPR and write output to /gpfs disk
$MPIRUN $MDRUN -v -nice 0 -np $NSLOTS \
-s n12_random_50_protein_all.tpr \
-o n12_random_50_protein_all.trr \
-c n12_random
Dear GMXers,
I'm trying to compute the surface tension between water and graphite
surface, using the C-O interaction parameters as in Werder et. al. J. Phys.
Chem. B 2003. The expected contact angle, based on Young's equation, is 86
degrees (as reported in Werder's paper by droplet method). The SP
Thanks everyone for the responses. I should have framed my question much
more precisely. I am trying to use the template.c code of (gmx_4.0.7) and
within this, I want to take care of PBC. To do this, I should be having the
knowledge of box dimensions. How can this done?
I also know that the g_ener
Thanks Tsjerk for the information. It would be very nice if you can
elaborate it. I am unable to understand.
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Thu, Dec 8, 2011 at 12:10 AM, Tsjerk Wassenaar wrote:
> Hi Chandan,
>
> Pretty simple; you just take the smallest distance between the time
Thanks Mark for the reply. I didn't find anything in AMBER manual. I
emailed the author of that paper.
I have one more question:
Whether *charged system correction
term*(-(1/(8*epsilon_0*kappa^2*L^3))*(Sum over q^2)) has been
implemented in the
PME implementation of Gromacs.
I am talking about t
>
> Thanks Tsjerk for the information. It would be very nice if you can
> elaborate it. I am unable to understand.
>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
>
>
> On Thu, Dec 8, 2011 at 12:10 AM, Tsjerk Wassenaar wrote:
>
>> Hi Chandan,
>>
>> Pretty simple; you just take the smallest di
Dear Sir,
I need to ask you that if I want only pdb coordinates in the resultant
md-noPBC.xtc/md-noPBC.pdb file rather than the solvant atoms and
coordinates then what should I do. because the water box causes very delay
in loading of frames and its difficult to viualize the trajectory. kindly
help
For any text file, use your favorite editor to delete all your water
molecules. It will load very fast. For the xtc/trr files, use trjconv with
an index file to write a new xtc/trr file without water molecules. Index
file should contain the atom nos. of the molecules you want.
trjconv -s a.tpr -f
On 8/12/2011 5:04 PM, Chandan Choudhury wrote:
For any text file, use your favorite editor to delete all your water
molecules. It will load very fast. For the xtc/trr files, use trjconv
with an index file to write a new xtc/trr file without water
molecules. Index file should contain the atom no
On 8/12/2011 2:54 PM, Chandan Choudhury wrote:
Thanks everyone for the responses. I should have framed my question
much more precisely. I am trying to use the template.c code of
(gmx_4.0.7) and within this, I want to take care of PBC. To do this, I
should be having the knowledge of box dimensio
On 8/12/2011 3:21 PM, Surya Prakash Tiwari wrote:
Thanks Mark for the reply. I didn't find anything in AMBER manual. I
emailed the author of that paper.
I have one more question:
Whether /charged system correction term/
(-(1/(8*epsilon_0*kappa^2*L^3))*(Sum over q^2)) has been implemented
in
Hi users,
Am running the mdrun_mpi on cluster with the md.mdp parameters as-
; VARIOUS PREPROCESSING OPTIONS
title= Position Restrained Molecular Dynamics
; RUN CONTROL PARAMETERS
constraints = all-bonds
integrator = md
dt = 0.002 ; 2fs !
nsteps = 250 ; total 5000 ps.
ns
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