hi dear GMX users
I simulated protein-ligand complex for 20 nanoseconds. I want to calculate free
energy by LIE method so I simulated ligand in water in the same conditions. I
used PME and full periodic boundary conditions in my simulations so I wrote a
new .mdp file that didn't use PME (I used
when you are creating the forcefield for cnt by g_x2top there you can
easily modify the sigma and epsilon value. For that you need to add some
values in ffnonbonden.itp file.
On Sat, Jan 11, 2014 at 7:07 AM, Justin Lemkul wrote:
>
>
> On 1/10/14, 6:14 PM, Michelle Aranha wrote:
>
>> Hi,
>>
>>
On 1/10/14, 6:14 PM, Michelle Aranha wrote:
Hi,
I am trying to simulate a simple system of CNT in bulk water.
The steps that I have completed are:
1. Create a pdb file for CNT.
2. Use editconf to convert to a gro file and define the length of the
simulation box, the pbc etc.
3. Create a forcef
On 1/10/14, 4:54 PM, Tom wrote:
Dear Gromacs Users,
We want to install Gromacs on a computer of 12 cores with highper threading
(virtual 24 cores) on the system of OpenSuse.
But we met the following error message:
-
Make Error at cmake/gmxManageMPI.cmake:161 (message):
MPI sup
On 1/10/14, 2:20 PM, Sidath Wijesinghe wrote:
Justin,
i was able to obtain the . top file for 3 uncharged monomers. then i used the
grompp
i got a fatal error as follows
Program grompp, VERSION 4.5.5
Source code file: grompp.c, line: 175
Fatal error:
The largest charge group contains 2
On 1/10/14, 12:37 PM, Michael Daily wrote:
Hi all,
I have been conducting simulations of peptoids (a cousin of peptides) in
implicit solvent in gromacs, which in conjunction with REMD has been very
useful for sampling the conformational distribution.
Since some of the peptoids are amphiphilic
Hi,
I am trying to simulate a simple system of CNT in bulk water.
The steps that I have completed are:
1. Create a pdb file for CNT.
2. Use editconf to convert to a gro file and define the length of the
simulation box, the pbc etc.
3. Create a forcefield folder in my current working directory
Dear Gromacs Users,
We want to install Gromacs on a computer of 12 cores with highper threading
(virtual 24 cores) on the system of OpenSuse.
But we met the following error message:
-
Make Error at cmake/gmxManageMPI.cmake:161 (message):
MPI support requested, but no MPI compiler
Justin,
i was able to obtain the . top file for 3 uncharged monomers. then i used
the grompp
i got a fatal error as follows
Program grompp, VERSION 4.5.5
Source code file: grompp.c, line: 175
Fatal error:
The largest charge group contains 207 atoms. The maximum is 32.
For more information
Hi all,
I have been conducting simulations of peptoids (a cousin of peptides) in
implicit solvent in gromacs, which in conjunction with REMD has been very
useful for sampling the conformational distribution.
Since some of the peptoids are amphiphilic, I'm also interested in
simulating them implic
You can use the code modification I indicated in that redmine post.
Chris.
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Lalita Shaki
Sent: 10 January 2014 03:43
To: gmx-users
Subject: Re: [gmx-users] pull_geometry=direction
Dear
Dear Christopher and gromacs users,
I consider using the pull_geometry = direction-periodic. nut this option
prevent me to use any pressure scaling, which I am not sure it is good for
my calculation.
Does someone can recommend me some literture about the effect of using the
NVT ensemble or the NP
When you run make_ndx there is a list of commands provided that allow you to
pick out the atoms you want. These atoms are then used to create new groups in
your index file. Further explanations and examples are provided if you enter h.
nr : group ! 'name' nr name 'splitch' nrEnter
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