Hey :)
The system needs to be energy minimized and relaxed after generation. Note
that the options -d and -x/-y/-z are exclusive. Only the latter will be
used.
Cheers,
Tsjerk
On Mar 11, 2014 6:47 AM, jhosamelly ducut_melsar...@yahoo.com wrote:
I want to generate a .gro file for a
On Tue, Mar 11, 2014 at 6:17 AM, Bappa Ghosh ab54...@gmail.com wrote:
Thanks Mark for your reply,
I am using gromacs version 4.6.3 with single precision.
Also I used state.cpt in mdrun , not in the tpbconv. I apologise for my
typing mistake.
Please use copy and paste when reporting
Dear users,
Is it absolutely essential to position restrain the
ligand during equilibration step before going for
production run for a protein-ligand simulation?
Thank you
Regards
Kavya
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PLUMED might be useful in this case : http://www.plumed-code.org
You could setup a simulation with
http://plumed.github.io/doc-v2.0/user-doc/html/_u_p_p_e_r__w_a_l_l_s.html to
achieve your goal.
Or, as Justin suggested, it might be more straightforward for you to slightly
modify the current
Thanks Mark. Yes, my ligand.itp indeed has both [atomtypes] entry as well
as [molecule] entry. I have followed the following procedure to #include
while creating my first molecule:
Run pdb2gmx command.
Added #include ligand.itp after
#include charmm27.ff/forcefield.itp
but before
[ moleculetype ]
Hi
I'm trying to set up a slightly modified version of swm4-ndp water with
anisotropic polarizibility. In contrast to sw-water, where the Drude
(shell) particle is connected to a dummy particle, it is connected to
the oxygen in swm4-ndp. In sw.itp, ananisotropic polarizibility is
defined
On 3/11/14, 7:27 AM, Peter Hamm wrote:
Hi
I'm trying to set up a slightly modified version of swm4-ndp water with
anisotropic polarizibility. In contrast to sw-water, where the Drude (shell)
particle is connected to a dummy particle, it is connected to the oxygen in
swm4-ndp. In sw.itp,
Dear all
I did 20 ns MD simulation on the system with many atoms (containing chain
a, b and c of protein). Unfortunately, I forgot to write energygrps (chain
a, b and c) in mdp file. My mdrun last long time.
Is there any way to obtain new edr file containing chain a, b and c.
Any help will
On 3/11/14, 8:53 AM, Atila Petrosian wrote:
Dear all
I did 20 ns MD simulation on the system with many atoms (containing chain
a, b and c of protein). Unfortunately, I forgot to write energygrps (chain
a, b and c) in mdp file. My mdrun last long time.
Is there any way to obtain new edr file
On Tue, Mar 11, 2014 at 1:30 PM, Archana Sonawani-Jagtap
ask.arch...@gmail.com wrote:
Hi Everyone,
I would like to know if we can run production MD simulation without
pressure coupling for protein-ligand simulation?
Yes. Whether that will produce something scientifically relevant is up to
Use mdrun -rerun on a trajectory with only the frames you care about, and
this time with the groups defined. This is how you should intend to do it,
because the combined running time will be shorter!
Mark
On Tue, Mar 11, 2014 at 1:53 PM, Atila Petrosian
atila.petros...@gmail.comwrote:
Dear
Dear Justin
Thanks for your quick reply.
I did before:
Thus, I should obtain new tpr file from new mdp file with the desired
energygrps:
grompp -f new.mdp -c *.gro -p *.top -o new.tpr
Then, I should use
mdrun -s new.tpr -o new.trr -e new.edr -rerun old.trr
Are my manner and commands true?
Excuse me
In previous post, sentence in line 3 (I did before:) is wrong.
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Thanks, Justin, for the quick response. Yes, I can see what to change
in gmxlib/bondfree.c
Best wishes
Peter
On 3/11/14, 7:27 AM, Peter Hamm wrote:
Hi
I'm trying to set up a slightly modified version of swm4-ndp water with
anisotropic polarizibility. In contrast to sw-water, where the
No default Angle types
--
*Mayank Kumar Dixit *
Molecular Dynamics lab
Department of Chemistry
IIT Bombay
Powai, Mumbai.
Mob No 9820697156
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Dear Sir,
I wish to inform you that when I am running the command
grompp then I am getting errors *No default Angle types* and No *default
Ryckaert-Bell. types*. Please suggest solutions as soon as possible
Thanks and warn regards
--
*Mayank Kumar Dixit *
Molecular Dynamics lab
On 3/11/14, 1:44 PM, Mayank Dixit wrote:
Dear Sir,
I wish to inform you that when I am running the command
grompp then I am getting errors *No default Angle types* and No *default
Ryckaert-Bell. types*. Please suggest solutions as soon as possible
You've defined interactions
On 3/11/14, 2:03 PM, ehs wrote:
Hi gmx users,
I have tried many ways to simulate a relatively long ionomer chain (340
atoms) solvated in about 100 water molecules, but I did not succeeded yet.
The ionomer length is mainly in x direction. For instance, I used the
following commands:
Thanks Justin.
I didn't use maxsol for this particular example.
How can force water to distribute evenly in the box? I thought energy
minimization could do it and but in my case, no success so far.
--
View this message in context:
On 3/11/14, 2:24 PM, ehs wrote:
Thanks Justin.
I didn't use maxsol for this particular example.
How can force water to distribute evenly in the box? I thought energy
minimization could do it and but in my case, no success so far.
I don't know about evenly, but you can do it randomly with
Hi,
When trying to run normal mdrun_mpi with Gromacs 4.6.3 on Bluegene/P, I met
this error:
Can not set thread affinities on the current platform. On NUMA systems this
can cause performance degradation. If you think your platform should support
setting affinities, contact the GROMACS developers.
Hi all
I have very simple query. While continuing simulations why we need to use
*.gro (-c) with grompp as *.cpt (-t) has all the information (as checked
with gmxcheck)?
cpt file should suffice all the purposes. I tried using grompp providing -t
*.cpt file but without -c *.gro file, it does not
On 3/11/14, 10:36 PM, gromacs query wrote:
Hi all
I have very simple query. While continuing simulations why we need to use
*.gro (-c) with grompp as *.cpt (-t) has all the information (as checked
with gmxcheck)?
cpt file should suffice all the purposes. I tried using grompp providing -t
I have done the subscription, hope my email will be accepted.
Sucharita Dey,PhD, Research Fellow, Cancer Science Institute of Singapore,
National University of Singapore. 14, Medical Drive, #12-01, Singapore 117599.
Tel: (65) 90355220, email: cs...@nus.edu.sg
Hi
I am testing one MD run using gromacs. 2 days back it ran fine. Today when
I ran the exactly same code again, it gave following error:
Increasing the number of cell to communicate in dimension X to 3 for the
first time
---
Program
Hai
I am trying to calculate torsional angles in DNA, for that first I
made angle.ndx file by using
mk_angndx -f prod.tpr -n angle.ndx -type dihedral
the out put angle.ndx is looks like as following
[ Phi=0.0_3_1.31 ]
12 2 3 412 2 31512 2 3
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