Dear gmx users,
I want to simulate popc in water. What I have done is:
1.Build the popc.top file using the popc.itp parameters and including gmx.ff,
lipid.itp and spce.itp in it as below;
; Include forcefield parameters
#include ./gmx.ff/forcefield.itp
; Include water topology
#include
Dear all,
will the new version 4.6 work together with CUDA 4.2? Would be good to
know, since this is needed for the new NVIDIA Gemini cards with Kepler
technology.
Thanks,
Basti
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The factor depends on the choice of your reaction coordinate, and since
g_wham doesn't care about it - it's not included.
It accounts for the change in volume when going from cartesian to
general coordinates and can be computed as -k_B * T * (d ln ( | J |) /
d_lambda), where lambda is the
On 4/25/12 2:07 AM, Shima Arasteh wrote:
Dear gmx users,
I want to simulate popc in water. What I have done is:
1.Build the popc.top file using the popc.itp parameters and including gmx.ff,
lipid.itp and spce.itp in it as below;
; Include forcefield parameters
#include
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Respected sir,
While i am running the gromacs always i am getting the
error Residue 'GNP' not found in residue topology database.Kindly tell me
the what the error means.
Suryanarayana Seera,
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gmx-users mailing listgmx-users@gromacs.org
On 4/25/12 8:19 AM, seera suryanarayana wrote:
Respected sir,
While i am running the gromacs always i am getting the
error Residue 'GNP' not found in residue topology database.Kindly tell me the
what the error means.
On Wed, Apr 25, 2012 at 11:43 AM, SebastianWaltz
sebastian.wa...@physik.uni-freiburg.de wrote:
Dear all,
will the new version 4.6 work together with CUDA 4.2? Would be good to
know, since this is needed for the new NVIDIA Gemini cards with Kepler
technology.
Yes it will. I would like to
Hello:
I am running a membrane simulation with gromacs and I wondering how
to deal with energygrps? Should I put protein and lipids into one
energygrps? Or I should leave the lipids stay with solvent and ions?
thank you very much
best
Albert
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On 4/25/12 10:07 AM, Albert wrote:
Hello:
I am running a membrane simulation with gromacs and I wondering how to deal with
energygrps? Should I put protein and lipids into one energygrps? Or I should
leave the lipids stay with solvent and ions?
You can divide the system in any way you like
hello Justin:
thank you very much for kind reply.
In gromacs tutorial I found that the author use the following paramters:
tc-grps= Protein DPPC SOL_CL; three coupling groups - more
accurate
comm-grps= Protein_DPPC SOL_CL
do you have any idea why did he use different
On 4/25/12 10:20 AM, Albert wrote:
hello Justin:
thank you very much for kind reply.
In gromacs tutorial I found that the author use the following paramters:
tc-grps = Protein DPPC SOL_CL ; three coupling groups - more accurate
comm-grps = Protein_DPPC SOL_CL
OK, just so we're clear:
hello Justin:
thank you very much for your such kind explanations. It is quite helpful.
I am wondering how many CPU did you usually use for the membrane
simulations? and how many ns/day can you get the best if CPU is not a
problem with Gromacs? I am very confused about this question since
Just a follow up on this problem.
I think it is known that there is some bug in the 1/viscosity calculation in
Gromacs version of 4.5.3. As shown in the following posts in the mailing
list:1. lists.gromacs.org/pepermail/gmx-users/2011-January/057596.html2.
On 4/25/12 10:49 AM, Albert wrote:
hello Justin:
thank you very much for your such kind explanations. It is quite helpful.
I am wondering how many CPU did you usually use for the membrane simulations?
and how many ns/day can you get the best if CPU is not a problem with Gromacs? I
am very
Hi all!!
I am running a MD simulation of a protein modelled by using modeller...and I
am getting an error in the grompp command.
The error reported was : Number of coordinates in coordinate file
(z_b4em.gro) does not match that of topology file (z.top). We are however
not able to run the nohup
On 4/25/12 12:45 PM, vinee2here wrote:
Hi all!!
I am running a MD simulation of a protein modelled by using modeller...and I
am getting an error in the grompp command.
The error reported was : Number of coordinates in coordinate file
(z_b4em.gro) does not match that of topology file (z.top).
Hi Gromacs Users,
I want to mutate a glutamate in my protein to alanine in presence of a
ligand.
With glutamate, the protein charge is -3. To neutralize the system, I added
3K+ ions.
Now when I mutate GLU to ALA, the charge in state_B will be +1 (protein -2
+ 3K+).
Right now I'm in the charge
Dear gmx users,
I may have a silly question, how to make a group of two atoms from the same
molecule?
e.g, I want to make an HN group of both H and N from my 2nd residue,
I know for single one, commands in *.dat file is like:
nameN = resnr 2 and name N;
nameH = resnr 2 and name H;
nameN;
On 4/25/12 9:19 PM, mu xiaojia wrote:
Dear gmx users,
I may have a silly question, how to make a group of two atoms from the same
molecule?
e.g, I want to make an HN group of both H and N from my 2nd residue,
I know for single one, commands in *.dat file is like:
nameN = resnr 2 and name
On 25/04/2012 3:24 PM, Albert wrote:
hello:
it is blue gene P. And the gromacs is single precision in the
cluster. Getting Loaded...And the administrator told me that I have to
use the multiples of 32 in the bg_size parameter. The number specified
in -np should be 4 times bg_size.
Yes,
Please do not make unsolicited general GROMACS inquiries to private
email addresses. The mailing lists exist for these kinds of purposes.
On point, you cannot be helped unless you provide the command lines that
you used and describe the objectives you were trying to achieve.
Whatever changes
On 25/04/2012 6:28 AM, PAVAN PAYGHAN wrote:
Dear Gromacs Users,
I am using gromacs version is 4.5.3.and running my jobs on single node
with 8 cores.
I have two different systems which contain about 425000 atoms (protein
+ Lipid +SOL) one with bound ligand
and another one unbound
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