Great! It's important to have all data validated carefully. Have you
put together a set of tests, with coverage of all the atom types and
interaction types, showing that the molecules give the same energies
in both GROMACS and AMBER? Validating conversions is quite important
so that people can tr
Dear All,
Reading the parameters for Gromos 53A6 ff ( article by Oostenbrink *et al.
Journal of computational chemistry* 25.13 (2004): 1656-1676.), I got
confused about van der waals interactions between non-bonded atoms.
for two atom types, we use combination rules to get (Cij 6) and (Cij 12),
On 12/10/15 6:01 PM, Man Hoang Viet wrote:
Dear GROMACS Admins,
I have implemented AMBER force field ff12SB and ff14SB into GROMACS and
want to share them with all gromacs users. I have tried to upload it via
below link
http://www.gromacs.org/Downloads/User_contributions/Force_fields
However,
On 12/10/15 12:29 PM, soumadwip ghosh wrote:
Thanks Justin for your reply. I was wondering then how to prepare an OH.itp
file from the scartch. Can it be made using pdb2gmx? Also from some old
It's already in ions.itp; you don't need to create anything.
threads I came accross that hydroxide
Dear GROMACS Admins,
I have implemented AMBER force field ff12SB and ff14SB into GROMACS and
want to share them with all gromacs users. I have tried to upload it via
below link
http://www.gromacs.org/Downloads/User_contributions/Force_fields
However, I can not do register to upload. Could you plea
Thanks Justin for your reply. I was wondering then how to prepare an OH.itp
file from the scartch. Can it be made using pdb2gmx? Also from some old
threads I came accross that hydroxide and hydroxonium ions are species
which dont obey classical dynamics. I would appreciate your thoughts on
this.
I
Hi,
If the molecules have been parameterized in OPLS/Amber and Charmm, going from
Charmm to OPLS/Amber is pretty straightforward, you just to build a topology
using the OPLS/Amber atom-types instead of Charmm that correspond to your
system (its just an elaborate find/replace exercise). For pep
Thanks for your reply Micholas,
The secondary structure constraints are used to "guide" the structure to a
known minimum so to speak and that particular structure is of interest to me. I
never worked with OPLS or Amber, is the process of working with them equivalent
to using charmm via gromacs
Hi,
I haven't tried to restrain secondary structure; however, it may be possible by
using a combination of dihedral, angle, and distance restraints (see section
4.3 in the manual). If you look up the DSSP . It would likely be cumbersome,
but it may be do-able. The question is if the results fro
I've been trying to run a gromacs simulation of alternating d/l cyclical
peptides (yes I know this is a dead horse that's been beat one time to many...)
and after a lot of experimentation I managed to get an initial setup working
via charmm gui. However, as the simulation progresses the structur
Dear Gromacs Users
I'm trying to study a molecule (my solute) in methanol as solvent.
For my solute I use Charmm27 ff, while for methanol I want to use opls/aa
ff.
I do this beacuse methanol is already implemented in opls force field.
My .top file is:
#include "charmm27.ff/forcefield.itp"
You can't use one force-field for one molecule and another force-field for
another. It doesn't make sense. Ethanol is implimented in Charmm, so I suspect
you can get methanol also.
-Micholas
===
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/O
On 12/10/15 10:49 AM, Daniele Veclani wrote:
Dear Gromacs Users
I'm trying to study a molecule (my solute) in methanol as solvent.
For my solute I use Charmm27 ff, while for methanol I want to use opls/aa
ff.
I do this beacuse methanol is already implemented in opls force field.
My .top fil
On 12/10/15 8:57 AM, soumadwip ghosh wrote:
Hi all,
I am trying to simulate a polymer membrane in the presence of
electrolytes. As an effort to corroborate experimental outcomes I have to
do simulation in the presence of 0.1M NaOH. I know that OH- is present in
the standard CHARMM FF
Hi all,
I am trying to simulate a polymer membrane in the presence of
electrolytes. As an effort to corroborate experimental outcomes I have to
do simulation in the presence of 0.1M NaOH. I know that OH- is present in
the standard CHARMM FF directory. So, I tried to add 15 Na (+) and 15 OH
Another quick note is that if gromacs was installed with mpi support the
default binary is not gmx but instead gmx_mpi (this could have been changed
during the configuration point in your install, but I would check if you have
gmx_mpi instead of gmx just in case).
===
Micholas
The force-field you generated for the ligand may not be perfect, and as a
result the ligand structure may alter during the energy minimization. Another
thing to check is did you remember to make your molecules whole again before
visualizing in vmd?
===
Micholas Dean Smith, PhD.
Hii Peter
Thank you for your valuable suggestion. I will check and ask you again
whether it is working or not.
Regards
Puneet
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of
gromacs.org_gmx
Thank you. I didn't change my file extension. I could get the ".xvg" file from
the ".trr" file, but I couldn't visualize the ".trr" file in VMD. It's weird. I
checked the file, it seemed normal.Checking file traj.trr trn version:
GMX_trn_file (single precision) Reading frame 0 time0.00
This is a unix/linux problem, not a gromacs problem.
And as such, I strongly suggest that you not run such commands as root, but
rather as an ordinary user.
Running commands as root, especially if you know little or no unix/linux can be
very dangerous.
The problem is probably in your path. The s
Hello
I am using command
"genrestr -f jz4.gro -o posre_jz4.itp -fc 1000 1000 1000" for Restraining
the Ligand but I am facing following error
[root@localhost AD]# gmx genrestr -f lig.gro -o lig.itp -fc 1000 1000 1000
bash: gmx: command not found
[root@localhost AD]# genrestr -f lig.gr
> On 10 Dec 2015, at 10:18, Felix W.-H. Weng wrote:
>
> Hi,
>
> Thank you for your patience.
>
> It seems that statutil.h is missing under both locations... I do see a
> stringutil.h under /usr/local/gromacs/include/gromacs/utility though, could
> that be used as a replacement for GROMACS 4.5.
Hi,
Thank you for your patience.
It seems that statutil.h is missing under both locations... I do see a
stringutil.h under /usr/local/gromacs/include/gromacs/utility though, could
that be used as a replacement for GROMACS 4.5.5?
Best,
Wei-Hsiang
>>>
Wei-Hsiang Weng (翁偉翔)
Hi,
> On 10 Dec 2015, at 08:59, Felix W.-H. Weng wrote:
>
> Dear all:
>
> Has anyone succeeded in installing the command g_correlation in GROMACS
> 4.5.5?
Does it work with 3.3?
> File obtained from http://www.mpibpc.mpg.de/grubmueller/g_correlation
> I tried installing but I keep getting the
Dear all:
Has anyone succeeded in installing the command g_correlation in GROMACS
4.5.5?
File obtained from http://www.mpibpc.mpg.de/grubmueller/g_correlation
I tried installing but I keep getting the error message seen below.
*6/include -I/usr/local/gromacs/bin/include/gromacs -c -o g_correlatio
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