Hello gmx users,
I need to use ATP's parameter for amber port in gromacs. The atp.prep and
frcmod.phos for ATP can be found at
http://www.pharmacy.manchester.ac.uk/bryce/amber. How can I use it in
ffamber.
The program amb2gmx.pl needs amber to be installed, which is not present.
Same with ACPYPI.
Amir Marcovitz wrote:
Thank you Justin,
actually, i have two parallel rigid plates that are free to move towards
each other on the Y-axis (i used position restrain on Y and Z axes)
later on i will umbrella sampling to obtain the plate-plate PMF at
various distances from each other (thanks a
Thank you Justin,
actually, i have two parallel rigid plates that are free to move towards
each other on the Y-axis (i used position restrain on Y and Z axes)
later on i will umbrella sampling to obtain the plate-plate PMF at various
distances from each other (thanks a lot for the helpful tutorial
grompp in 4.0.7 doesn't use the -np flag anymore. You don't need it.
In your example just do this:
grompp_mpi -v -f _ _ _
mdrun_mpi -v -f -deffnm -np
-Matt-
edmund lee wrote:
Dear all,
I am new in Gromacs 4.0.7 before this I was using the GROMACS 3.3.3.
I have some doubt in the grompp
edmund lee wrote:
Dear all,
I am new in Gromacs 4.0.7 before this I was using the GROMACS 3.3.3.
I have some doubt in the grompp commands when i want to run in parallel
In Gromacs 3, I just use:
grompp_mpi -v -f _ _ _ -np 4
then,
mdrun_mpi -v -f -deffnm -np 4
but in Gromacs 4, I cant u
Dear all,
I am new in Gromacs 4.0.7 before this I was using the GROMACS 3.3.3.
I have some doubt in the grompp commands when i want to run in parallel
In Gromacs 3, I just use:
grompp_mpi -v -f _ _ _ -np 4
then,
mdrun_mpi -v -f -deffnm -np 4
but in Gromacs 4, I cant use 4 nodes in grompp
nishap.pa...@utoronto.ca wrote:
Hi,
I am trying to extend my simulation time from 100ns -> 300ns. So I
used the command :
tpbconv -s old.tpr -extend 10 -o new.tpr
but I got this:
Extending remaining runtime of by 20 ps (now 14992 steps)
Writing statusfile with starting step
Miguel Quiliano Meza wrote:
Hi everyone.
Nowadays I am learning how to analyze my results after MD. I have been
reading the tutorial "GROMACS Tutorial for Drug – Enzyme Complex" and
all is fine but I have a big doubt about g_rms. I know that g_rms
compares two structures by computing the ro
Hi,
I am trying to extend my simulation time from 100ns -> 300ns. So I
used the command :
tpbconv -s old.tpr -extend 10 -o new.tpr
but I got this:
Extending remaining runtime of by 20 ps (now 14992 steps)
Writing statusfile with starting step 0 and length 14992
Hi everyone.
Nowadays I am learning how to analyze my results after MD. I have been
reading the tutorial "GROMACS Tutorial for Drug – Enzyme Complex" and all is
fine but I have a big doubt about g_rms. I know that g_rms compares two
structures by computing the root mean square deviation (RMSD). In
Amir Marcovitz wrote:
Hi,
i'm simulating a surface in water and ions which is composed of 6X6
Carbon atoms arranged on a 2-d lattice. (using ffamber99)
i want to keep the spacing between C-C neighbouring atoms at 0.34
Angstrom (or some other spacing of choice..), and to maintain the
surfac
Hi,
i'm simulating a surface in water and ions which is composed of 6X6 Carbon
atoms arranged on a 2-d lattice. (using ffamber99)
i want to keep the spacing between C-C neighbouring atoms at 0.34 Angstrom
(or some other spacing of choice..), and to maintain the surface rigid and
planar
for that i
> fairuz zulkifli wrote:
>> Hello everybody,
>> I'm Fairuz from Malaysia.
>> I just want to ask if there is someone that have information about
>> PDB of ice and itp file of ice.
>> I only had PDB of the ice and trying to convert it into itp file
>> using GAMESS software.
>
> You can't. A .pdb fi
fairuz zulkifli wrote:
Hello everybody,
I'm Fairuz from Malaysia.
I just want to ask if there is someone that have information about PDB
of ice and itp file of ice.
I only had PDB of the ice and trying to convert it into itp file using
GAMESS software.
You can't. A .pdb file is a coordinat
Hello everybody,
I'm Fairuz from Malaysia.
I just want to ask if there is someone that have information about PDB of
ice and itp file of ice.
I only had PDB of the ice and trying to convert it into itp file using
GAMESS software.
Is there any suggestion?
Thank you.
--
gmx-users mailing listgmx
Hi all
I am doing some tests with the CHARMM port in GROMACS. Before to start
more extensive simulations with this ff
I have performed a short run of 1000 TIP3-CHARMM water molecules in a
cubic during at T=300 K and P=1.015 bar with v-rescale and PR as
thermostat and barostat. I have used the
On 05/02/10 00:43, vivek sharma wrote:
Hi Mark,
Thanks for your response, it worked well for few molecule but not for all.
As I mentioned first I am doing docking and then processing receptor
through pdb2gmx and ligand through PRODRG server.
But number of Hydrogen atoms in docked ligand and PRODR
Hi Mark,
Thanks for your response, it worked well for few molecule but not for all.
As I mentioned first I am doing docking and then processing receptor through
pdb2gmx and ligand through PRODRG server.
But number of Hydrogen atoms in docked ligand and PRODRG generated topology
are not same. Althou
Hi Tsjerk,
Thanks for your response,
I am finding problem in using original coordinates with the PRODRG topology
because of mismatch in number of Hydrogen atoms in original coordinate file
and PRODRG topology.
Can you tell me how can I try 2nd option you suggested i.e. Fit the
structure obtained fr
On 04/02/10 21:01, 011013021-Jyotsna wrote:
Dear Mark,
Your suggestions were very helpful .
As per the literature I am following , It is required that the dummy
atom has mass 0 and charge -0.950.Hence , I created the following itp
file with this in mind.
##
; topology for hydrogen.
[ molecul
Hi Catarina,
This file contains the parameters for MD run, e.g. timestep, number of
steps, etc.
Good luck with IL,
Vitaly
--
Vitaly V. Chaban, Ph.D.
http://www-rmn.univer.kharkov.ua/chaban.html
On Thu, Feb 4, 2010 at 2:39 PM, Catarina Nunes wrote:
> Sorry Vitaly,
> Can you tell me what mean
Dear Mark,
Your suggestions were very helpful .
As per the literature I am following , It is required that
the dummy atom has mass 0 and charge -0.950.Hence , I
created the following itp file with this in mind.
##
; topology for hydrogen.
[ moleculetype ]
;namenrexcl
H2 2
[ at
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