Dear gmx user
when we run MD by mdrun tool in gromacs
IS there is any option in command prompt to include and controll the number of
processor ? otherwise will it automatically use all available processor?
Because i am using pentum Intel i5 processor
When i run MD will
Hi
Take a look to mdrun -nt flag to set the number of threads. Otherwise
the default is guessed according to the description displayed by mdrun
(what effectively means to take all available ones, I think).
There are several related entries in the mailing list. Keep in mind that
thread-based
Dear Gromacs Users,
I have been trying to simulate a protein in implicit solvent. When I used a
single processor by setting -nt to 1 , I did not encounter any problem. But
when I tried to run the simulations using more than 1 processor I get the
following error.
Fatal error:
Constraint dependenc
Ozlem Ulucan wrote:
Dear Gromacs Users,
I have been trying to simulate a protein in implicit solvent. When I
used a single processor by setting -nt to 1 , I did not encounter any
problem. But when I tried to run the simulations using more than 1
processor I get the following error.
Fata
Dear Justin,
Thanks for the fast response. The exact command I used is :
mdrun -v -s eq2.tpr -deffnm eq2 -g eq2.log -nice 19 >& eq2.out &
Regards,
Ozlem
On Wed, May 4, 2011 at 3:23 PM, Justin A. Lemkul wrote:
>
>
> Ozlem Ulucan wrote:
>
>>
>> Dear Gromacs Users,
>>
>> I have been trying to s
Ozlem Ulucan wrote:
Dear Justin,
Thanks for the fast response. The exact command I used is :
mdrun -v -s eq2.tpr -deffnm eq2 -g eq2.log -nice 19 >& eq2.out &
This is for a serial run. There's no problem with this (except that -s and -g
are redundant with -deffnm, but that's not an issue)
On 4/05/2011 11:23 PM, Justin A. Lemkul wrote:
Ozlem Ulucan wrote:
Dear Gromacs Users,
I have been trying to simulate a protein in implicit solvent. When I
used a single processor by setting -nt to 1 , I did not encounter any
problem. But when I tried to run the simulations using more tha
Dear Justin, this was only a test run and I ran the simulations on my
multi-core workstations (4 cores actually). MPI is no longer required for
such a situation. Since I did not set -nt option to 1, this can be accepted
as a parallel run. So the command I sent in my previous e-mail was for the
para
Hi!
If you are running implicit solvent with no cutoffs, ie using the special
all-vs-all kernels, then particle decomposition will be used. This exact
combination (gb, all-vs-all, dd) is quite tricky to implement, and is not
supported at the moment, IIRC.
This could be documented better, sorry
Hi all
I have performed a PMF simulation of taking part of a molecule out of
the cavity of a host using umbrella sampling. The free energy curve
suggests that the guest prefers to be outside the host as the bound
state is higher in energy, or the free energy difference to go in is
positive. Howeve
Thank you very much for the suggestions, I will try both and compare the
results.
On Wed, May 4, 2011 at 4:13 PM, Per Larsson wrote:
> Hi!
>
> If you are running implicit solvent with no cutoffs, ie using the special
> all-vs-all kernels, then particle decomposition will be used. This exact
> co
Dear gmx-users,
I have a cube (8 nm) of the system containing 1:1 :: water: methanol, a
polypeptide, Li ions and 2,5-dihydroxybenzoic acid anions.
I am heating this system with no PBC ( evaporation).
The md.mdp file is:
; Run parameters
integrator = md ; leap-frog integrator
nsteps =
shivangi nangia wrote:
Dear gmx-users,
I have a cube (8 nm) of the system containing 1:1 :: water: methanol, a
polypeptide, Li ions and 2,5-dihydroxybenzoic acid anions.
I am heating this system with no PBC ( evaporation).
The md.mdp file is:
; Run parameters
integrator = md ; leap-f
Your windows are restrained. The PMF that you get out of WHAM is a
representation of the relative sampling after removing the umbrella
biases. Sounds like you are saying that you look at the still-biased
trajectories and you see different a different distribution of states
than you do in th
Hi Chris
My windows are restrained obviously using the force constant in the mdp
file. The trajectories that I have viewed are those of the individual
biased sampling windows. I have not put on the unbiased simulations yet.
There is also the following issue: The simulations involve two identical
m
yes it will, and so will it affect the profile if water molecules or
ions go in when both chains are absent.
You'll need to determine what question you are trying to answer and
also think pretty hard about what your PMF really means in the context
of this system.
Chris.
-- original messa
Hello all,
I have written a script that does per-time-step coloring of the water
molecules, residues, and ions in my protein based on electric field values I
previously calculated. I received excellent help here a few months sorting
out some problems with the script, but there is one big one remai
The current simulations are currently in vacuum. Does the following mdp
file seem ok. Note that this is a production run using the final
configuration after a lengthy equilibration. Also I was thinking about
trying to prevent the other chains from entering the specific site; is
there a a way to imp
Dear Gavin:
I'm not seeing a lot of effort on your part to answer these questions.
I suspect that you can answer some of this. Good luck!
Chris.
-- original message --
The current simulations are currently in vacuum. Does the following mdp
file seem ok. Note that this is a production run us
Hello,
I have calculated the cumulative number from -cn for the usnic acid solvated by
methanol molecules, but this result is enough different to those obtained by
integration of the 4*pi*(number density)*area(gr. r2dr) until the first minimum
of the RDF. I would like to know how the cumulative
Hi,
When i used g_sgangle, i specified 2 index groups of 3 atoms each and gave
the -oa flag to get the angle between them. I got two columns of output
(besides the time index) - one with much larger values on the right (they
look reasonable) and one with much smaller values on the left. what is th
nevermind its just the cosine
On Wed, May 4, 2011 at 3:36 PM, jeremy adler wrote:
> Hi,
>
> When i used g_sgangle, i specified 2 index groups of 3 atoms each and gave
> the -oa flag to get the angle between them. I got two columns of output
> (besides the time index) - one with much larger value
Hello, everyone,
Does anyone have experience of doing NVE simulation? I wish to know, for a
system with box size 6.1*6.1*6.1nm, whether the microcanonical ensemble for
a NVE simulation will converge with the canonical ensemble from a NPT
simulation?
Thanks,
--
gmx-users mailing listgmx-users
I'm not sure about the V vs. P part, but the E vs. T part depends on
the thermostat that you use. For some thermostats, the problem can be
large: http://www.ncbi.nlm.nih.gov/pubmed/20046980
-- original message --
Does anyone have experience of doing NVE simulation? I wish to know, for a
syst
Hi dear gmx-users and developers,
I'm working on a system involved with solid surface and solution, which using
periodic boundary conditions in x and y directions only.
I need to creat a virtual wall at both z=0 and z=z, but it should be a
reflecting boundary conditions wall.
It's like this:
pr
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