On Jun 12, 2009, at 4:27 AM, lammps lammps wrote:
When I use CG martini force field to do simulation, and use the
example of Martini website.
There are many warnings when grompp the mdp file:
--
WARNING 4 [file mem16.top, line 41]:
For proper thermostat integration tau_t (0.1)
Ms. Aswathy S wrote:
Hi,
i would like to do a ligand -receptor simulation using OPLS-AA force field. I
suppose using the options in Gromacs I can create the itp files for protein
only. But how can i create the OPLS --AA topology file for the ligand. I think
PRODRG server only creates gromacs
Mark Abraham wrote:
Ms. Aswathy S wrote:
Hi,
i would like to do a ligand -receptor simulation using OPLS-AA force
field. I suppose using the options in Gromacs I can create the itp
files for protein only. But how can i create the OPLS --AA topology
file for the ligand. I think PRODRG server
Hi,
thanks for the help till now..
Now I got a problem that an equilibration step of 20 ps shows an error as
follows when i run grommp.
ERROR: pressure coupling not enough values (I need 1)
Please find the md.mdp file that I have used for this step.
thanks,
Aswathy
Dept. Biotechnology
Ext.
Ms. Aswathy S wrote:
Hi,
thanks for the help till now..
Now I got a problem that an equilibration step of 20 ps shows an error as
follows when i run grommp.
ERROR: pressure coupling not enough values (I need 1)
Please find the md.mdp file that I have used for this step.
You haven't spec
Hostfile should look like:
master slots=4 max-slots=4
compute-0-0 slots=4 max-slots=4
compute-0-1 slots=4 max-slots=4
compute-0-2 slots=4 max-slots=4
compute-0-3 slots=4 max-slots=4
compute-0-4 slots=4 max-slots=4
compute-0-5 slots=4 max-slots=4
compute-0-6 slots=4 max-slots=4
so its format is:
I have specified ref_p as 1, now grommp works fine.but show the error as below.
From the previous post what I understood is this is a problem with the gromacs
version. I am using Gromacs3.2.1. Is that could be the problem??
Back Off! I just backed up minim+ener.edr to ./#minim+ener.edr.2#
start
Ms. Aswathy S wrote:
I have specified ref_p as 1, now grommp works fine.but show the error as below.
From the previous post what I understood is this is a problem with the gromacs
version. I am using Gromacs3.2.1. Is that could be the problem??
Well, there certainly have been improvements
Thank you for your reply,
I was just struggling to get the ffxxxbon.rtp syntax right since I only
have atom distances to create the bonds.
So can anyone tell me what the correct syntax is for these defines in
the ffxxxbon.rtp file?
#define
Furthermore where and how can I add the angle inf
abelius wrote:
Thank you for your reply,
I was just struggling to get the ffxxxbon.rtp syntax right since I only
have atom distances to create the bonds.
So can anyone tell me what the correct syntax is for these defines in
the ffxxxbon.rtp file?
#define
? = force constant
Furtherm
But How can I determine this constant? (I guess using the one of normal
TRP would make no sense)
Thanks,
Abel
Justin A. Lemkul wrote:
abelius wrote:
Thank you for your reply,
I was just struggling to get the ffxxxbon.rtp syntax right since I
only have atom distances to create the bonds
abelius wrote:
But How can I determine this constant? (I guess using the one of normal
TRP would make no sense)
I would suggest reading the primary literature for your force field of interest.
How did the original authors assign these parameters? Usually bonded
information comes from ex
Since the charges / bond lengths and angles were obtained for QM
calculations for the excited state of TRP I'm wondering if it would make
sense to apply the alternative bond lengths and keep the force constants
of TRP in the ground state?
Cheers,
Abel
Justin A. Lemkul wrote:
abelius wrote:
Hi all
I need to avoid that a solute molecule cross to the other side of my
lipid bilayer.and I have thought in several alternatives, which I'm
not sure whether they are posible in gromacs so I decided to ask for
suggestions.
Could anyone give any possible alternative to restrict the move
Hi,
It is plain 10-4.
The difference is probably due to the coefficients.
With 10-4 mdrun integrates with a uniform atom density on the wall plane.
The tables simply use the table times the C12 and C6 parameters
without any other factor.
Berk
> Date: Thu, 11 Jun 2009 17:34:10 -0700
> From: ttru
Hi all,
I have noticed that there is a problem with the NH2 directive in ffG53a5.rtp and
ffG53a5.rtp. The following lines are incorrect:
[ impropers ]
-C -O N -CA gi_1
N H H -C gi_1
They refer to the H atoms by type, not name. They should instead read:
[ impropers ]
-C -O
Justin A. Lemkul wrote:
Hi all,
I have noticed that there is a problem with the NH2 directive in
ffG53a5.rtp and ffG53a5.rtp. The following lines are incorrect:
Edit: that should read "ffG53a5.rtp and ffG53a6.rtp"
-Justin
[ impropers ]
-C -O N -CA gi_1
N H H -C gi_1
They
hi all,
i am interested in doing full ab initio molecular dynamics using
gromacs, coupled to either GAMESS or Gaussian. i am not interested in
using any single or multilayer QM/MM scheme. it doesn't appear that
gromacs supports a full QM system. does anyone know the origin of this
limitation? or,
Alberto Sergio Garay wrote:
Hi all
I need to avoid that a solute molecule cross to the other side of my
lipid bilayer.and I have thought in several alternatives, which I'm not
sure whether they are posible in gromacs so I decided to ask for
suggestions.
In a periodic system with one symmetr
Anthony Costa wrote:
hi all,
i am interested in doing full ab initio molecular dynamics using
gromacs, coupled to either GAMESS or Gaussian. i am not interested in
using any single or multilayer QM/MM scheme. it doesn't appear that
gromacs supports a full QM system. does anyone know the origin o
Hi,
I have upgraded my gromacs version to 3.3.3 from 3.2.1. When I tried to run the
pdb2gmx i got the follo: error. From the previous post I guess that i should
edit this ffG43a1.hdb. but my input is a protein file so ..so is this necessary
or any other way to rectify this problem???
-
21 matches
Mail list logo
