Can anyone tell me how to make a mdp file for gromacs mdrun on NVIDIA GPU
card, the following is a mdp file which runs well on cpu, but when I add the
option "-testverlet" to mdrun in order to run it on GPU, it returns error
"nonbond potiential is not supported". Could you check the mdp fil
Dear gromacs users,
Can anyone tell me how to make a mdp file for gromacs mdrun on NVIDIA GPU card,
the following is a mdp file which runs well on cpu, but when I add the option
"-testverlet" to mdrun in order to run it on GPU, it returns error "nonbond
potiential is not supported". Could
Hi,
I want extract one frame from NPT to run MD
because for md need npt.gro and npt.cpt
So, if can we extract cpt of one frame?
and because I want to check if this frame at equilibration state, use
g_energy -f npt.edr
So, if can we extract edr of one frame?
Thank you very much!
maggin
On 6/20/13 11:11 PM, Hari Pandey wrote:
Hi all gromacs users
I have following (NVT.mdp) (NPT.mdp) and (NVE.mdp) . I have three parts of
system, A, B and C.
I want to put thermostat on A and C and couple the tempereture and do not put
any thermostat on B.
What I want is: after some ps,
Hi all gromacs users
I have following (NVT.mdp) (NPT.mdp) and (NVE.mdp) . I have three parts of
system, A, B and C.
I want to put thermostat on A and C and couple the tempereture and do not put
any thermostat on B.
What I want is: after some ps, temperature of A and C should be constant (
Please keep the discussion on the gmx-users mailing list; I am not a private
tutor. Comments embedded below.
On 6/20/13 8:35 PM, Hari Pandey wrote:
Hi Justin,
Thanks for last help.
I have following (NVT.mdp) (NPT.mdp) and (NVE.mdp) . I have three parts of
system, A, B and C.
I want to
Dear Anh,
You need to construct a .tpr file for the mdrun -rerun with:
- a .gro file with the ligand to be inserted at the end, which _must_ be
geometrically centered at 0,0,0 ;
- a matching .top file (which means with the ligand topology
appropriately inserted) ;
- a .mdp file wit
On 6/20/13 5:01 PM, Hari Pandey wrote:
Hi ,
How do I solve this problem in GROMACS:
I have a system with 3 part A,B and C
I have to put thermostat for A and C but not for B.
Gromacs display error, what is temperature for B.
How do aI decouple part B
Per the manual:
"tau-t: [ps]
tim
On 6/20/13 1:57 PM, Raji Viswanathan wrote:
I am new Gromacs user and I found Dr. Kerrigan's tutorial on the spider toxin
peptide. I was going through the steps in the tutorial but got stuck with the
genion command. When I am prompted to select a group, I get the error that it
is not found
Hi ,
How do I solve this problem in GROMACS:
I have a system with 3 part A,B and C
I have to put thermostat for A and C but not for B.
Gromacs display error, what is temperature for B.
How do aI decouple part B
thanks for help
Hari
--
gmx-users mailing listgmx-users@gromacs.org
As far as I know it should not be included. Make a tpr file new .top and
input file and run the mdrun with -rerun option as described here. "
http://manual.gromacs.org/online/mdp_opt.html#run";
Cheers,
Rajesh
On Thu, Jun 20, 2013 at 3:08 PM, Phan, Anh T. wrote:
> Dear GMX Users,
> My name is
Dear GMX Users,
My name is Anh Phan, a PhD student at University of Oklahoma.
I would like to calculate excess chemical potential of one gas molecule in
water solvent using Widom test particle insertion with Gromacs.
In this method, I will insert this gas molecule at a random position in each
con
I am new Gromacs user and I found Dr. Kerrigan's tutorial on the spider toxin
peptide. I was going through the steps in the tutorial but got stuck with the
genion command. When I am prompted to select a group, I get the error that it
is not found. I tried many different ways of specifying thi
Hi Oliver -
Hmm. Did you try to start from (a little bit) different configurations
on the problematic machine? Or re-install gromacs there, perhaps?
Dr. Vitaly Chaban
On Thu, Jun 20, 2013 at 3:44 PM, Oliver Schillinger
wrote:
> Dear Gromacs users,
>
> I experience a very strange problem
Dear Gromacs users,
I experience a very strange problem.
I have a well equilibrated system consisting of a protein, a ligand,
ions and water. On most machines I run my simulations on, everything is
just fine. Except for one compute cluster, where the system undergoes an
extreme expansion when
Justin Lemkul wrote
>>
>
> What was the outcome of EM before this? What if you try NVT before NPT?
> Have
> you tried reducing the timestep or the value of nstlist?
>
> I would try everything with ref_p = 1.0 instead of zero to make sure you
> can get
> a "normal" setup to work.
>
> -Justin
Hi,
g_rmsf doesn't do distances. To answer the question, you can use g_rms with
-fit none and a suitable index group. Does depend a bit on what you mean
with distance. The distance traveled by a residue could well mean the
average distance for all particles in the residue, which is what you'll get
Hi Natalie,
You might want to look into g_rmsf, used to calculate the root mean squared
fluctuation of atoms or residues.
sample usage: g_rmsf -f trajectory.xtc -s struc_mass.tpr -oq rmsf.pdb -o
rmsf.xvg
Additional commands of interest:
-res (when true, calculates residues as a whole)
-b (first
Thanks Mark and Baptiste, yes its case insensitive for atomtype names. I
have changed all names and its working now :-)
regards,
On Thu, Jun 20, 2013 at 2:55 PM, Baptiste Demoulin
wrote:
> Hi,
>
> GROMACS is indeed case insensitive when it comes to atomtypes. I had the
> same problem a while ag
Hi,
GROMACS is indeed case insensitive when it comes to atomtypes. I had the
same problem a while ago. The simplest way to deal with it is just to add a
letter at the end of your atomtypes.
2013/6/20 Mark Abraham
> Probably
>
> Mark
> On Jun 20, 2013 11:42 AM, "gromacs query" wrote:
>
> > D
Probably
Mark
On Jun 20, 2013 11:42 AM, "gromacs query" wrote:
> Dear All,
>
> I have a complex A-B (not covalent bonded)
>
> I want to use oplsaa.ff atom types original for A and all are in .top files
> in which some parameters are changed and I have another directory with
> modified just atomt
Hi guys,
What is the best way of calculating how far a residue has traveled from its
starting position during a simulations?
Thanks
Natalie
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Dear All,
I have a complex A-B (not covalent bonded)
I want to use oplsaa.ff atom types original for A and all are in .top files
in which some parameters are changed and I have another directory with
modified just atomtype names oplsaa.ff files (for B) that is ffbonded.itp,
ffnopnbonded.itp, atom
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