leila karami wrote:
Hi
in which case in mdp file, gen_vel should be yes or no?
... when you want to generate velocities or not. See manual section 3.4,
particularly 3.4.1
Mark
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please sea
Hi
in which case in mdp file, gen_vel should be yes or no?
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use th
Thanks Mark and Justin for all your input. I will try the git version and
do any necessary modifications to test my install.
> Yirdaw, Robel Birru wrote:
>> Thank you both for your reply.
>>
>> So how did you guys verify and test gromacs on your machines?
>> Mark, from your response, test-set 4
Stefan Hoorman wrote:
Stefan Hoorman wrote:
> How can I calculate the angle between a helix inserted in a
membrane and
> the axis perpendicular to the surface of the membrane. I have tried
> using g_helixorient, but the graphs all come as a straight line
in zero.
shivkumar bale wrote:
Hi Gromacs Users,
when I am trying to run the simulation I am getting the following error:
mpispawn.c:303 Unexpected exit status
Child exited abnormally!
Killing remote processes...DONE
I read about this online and it says that simulation is running out of
memory and
Hi Gromacs Users,
when I am trying to run the simulation I am getting the following error:
mpispawn.c:303 Unexpected exit status
Child exited abnormally!
Killing remote processes...DONE
I read about this online and it says that simulation is running out of
memory and it depends upon the grid sp
This kind of problems can occur if you were restraining atom positions and using
pressure coupling.
Best regards
Lucio.
Lucio Ricardo Montero Valenzuela
PhD Student
Laboratorio del Dr. Federico Sánchez
Ext. 27666
Departamento de Biología Molecular de Plantas
Instituto de Biotecnología, UNAM
Cu
Hi Elad,
This has been mentioned several times before, in a different context.
But fitting only affects coordinates, and not the PBC. So after
fitting the coordinates and the PBC don't match any more and any
analysis requiring PBC, such as calculating minimal distances, will
give garbled results.
Steven Ari Beasley wrote:
has anyone successfully incorporated dihedral angle restraints in
gromacs 4.0.5 protein simulation. i can only find instructions for
gromacs 3.3.1, nothing in the manual.
Do these instructions not work?
http://www.gromacs.org/Documentation/How-tos/Dihedral_Rest
has anyone successfully incorporated dihedral angle restraints in gromacs 4.0.5
protein simulation. i can only find instructions for gromacs 3.3.1, nothing
in the manual.
i don't know if the format is the same or whether it requires diffent .mdp
flags, but so far i have not been able to suc
Hi all,
I have a system of protein+water+ions.
I measured the minimum distance between one of the ions to the protein.
Afterwards I fitted the trajectory using g_trjconv -fit rot+trans
Did the same mindist again and the graphs are not always identical.
Any suggestions?
I use gromacs 4.0.5 wit
Thanks for your response.
I see that what I want to do is a little bit unusual. It is part of a bigger
picture that also include implicit water calculations and the main goal is to
look into the effects of water models on the results, not necessarily trying to
reproduce the experimental results
> Stefan Hoorman wrote:
> > How can I calculate the angle between a helix inserted in a membrane and
> > the axis perpendicular to the surface of the membrane. I have tried
> > using g_helixorient, but the graphs all come as a straight line in zero.
>
> See -z in g_sgangle -h
>
> Mark
>
>
> Thank y
pawan raghav wrote:
While running MD simulation I have number of queries mentioned below:
1. When executing xmgrace command it returns the bash command not found,
then how to install GRACE package on windows?
Visit the Grace website and follow whatever download and installation
instructio
While running MD simulation I have number of queries mentioned below:
1. When executing xmgrace command it returns the bash command not found,
then how to install GRACE package on windows?
2. When defining the box dimention then how do I know about the distance of
protein (207 residues) from the b
Hi Tatiana,
If you just want to estimate the binding energy, I suggest that,
initially, you use docking methodologies. For example, you can
use AutoDock program, that is a free program.
I hope this help
Osmair
Brazil
> Date: Fri, 4 Dec 2009 09:25:56 +0100
> From: r.fried...@bioc.uzh.ch
> To:
Hi,
I don't know.
I have not understood what you want to do.
On the physical level, there is no distinction between intra-molecular bonded
and non-bonded interactions. So this makes me suspect that what you are
trying to do is incorrect, independently of if you remove the 1-4's or not.
Berk
Dat
Hi,
Yes, RF in the couple scheme is correct.
The "manual" calculation you did is incorrect.
In the decoupled state the intra-molecular interactions of the decoupled
molecule should not be RF, but plain Coulomb.
The couple option does this correctly.
Berk
> Date: Fri, 4 Dec 2009 15:52:58 +0300
>
Dear gmx users,
I calculated the hydration free energy of benzene molecule two times.
First time I used a decoupling method implemented in GROMACS. Second
time I performed thermodynamical integration between different
topologies of the benzene molecule: non-interacting with media and
normal one. Al
Justin A. Lemkul ha scritto:
As per the title. I need to understand what is the difference to help
myself debug my inane efforts at CG parametrization. LJ(1-4) I think is
clear (non bonded, non-coulombic interactions between 1-4 pairs
described in the topology), but about the re
Vitaly V. Chaban wrote:
Hi,
Please suggest why is the reason that 1-4 term is not displayed (to be
selected for calculation) in the g_energy utility? I have two kinds of
objects (with 25 and 5 atoms) in my system - with "nexcl" equal to 3
and 2. I guess the 1-4 term may not be displayed if there
Hi Alan,
Thank you for all your efforts. This is getting strange, I tried
following your procedure below but is still does not work for me:
step 3500, will finish Fri Dec 4 09:56:51 2009Warning: 1-4 interaction
between 6 and 10 at distance 1.454 which is larger than the 1-4 table
size 1.000 nm
Dear Tatiana,
In principle you can estimate binding free energy differences using LIE
(or LIECE). Your success will depend on the protein and proper
parameters. The best way is to try ligands with known binding energies
at first. Check the relevant literature for details and parameters.
Ran.
--
23 matches
Mail list logo