On 12/04/2012 05:09 PM, Mark Abraham wrote:
2fs is normally considered too large a time step for stable integration
with only bonds to hydrogen constrained, so your observation of
non-reproducible LINCS warnings is not indicative of some other problem.
Sorry, but why is this whole setup running on my local desktop with
GPUs? As far as I know this is a rather typical set of parameters.
The only difference what I can think of is that gromacs was compiled
with intel and mkl libs on the cluster there as it was compiled with gcc
and fftw3 libs on the local desktop.
Sebastian
Also, if you ran your CPU-only calculations with nstlist=25 then AFAIK this
works fine, but is inefficient.
Mark
On Tue, Dec 4, 2012 at 3:41 PM, sebastian<
sebastian.wa...@physik.uni-freiburg.de> wrote:
On 11/23/2012 08:29 PM, Szilárd Páll wrote:
Hi,
On Fri, Nov 23, 2012 at 9:40 AM, sebastian<
sebastian.wa...@physik.uni-**freiburg.de<sebastian.wa...@physik.uni-freiburg.de>>
wrote:
Dear GROMCS user,
I installed the git gromacs VERSION 4.6-dev-20121117-7a330e6-dirty on my
local desktop
Watch out, the dirty version suffix means you have changed something in
the
source.
(2*GTX 670 + i7) and everything works as smooth as possible. The outcomes
are very reasonable and match the outcome of the 4.5.5 version without
GPU
acceleration. On our
What does "outcome" mean? If that means performance, than something is
wrong, you should see a considerable performance increase (PME,
non-bonded,
bondeds have all gotten a lot faster).
With outcome I mean the trajectory not the performance.
cluster (M2090+2*Xeon X5650) I installed the VERSION
4.6-dev-20121120-0290409. Using the same .tpr file used for runs with my
desktop I get lincs warnings that the watermolecules can't be settled.
The group kernels have not "stabilized" yet and there have been some fixes
lately. Could you please the latest version and check again.
I installed the beta1 release and still the water can not be settled.
Additionally, you could try running our regression tests suite (
git.gromacs.org/**regressiontests<http://git.gromacs.org/regressiontests>)
to see if at least the tests pass with the
binaries you compiled
Cheers,
--
Szilárd
Cheers,
Sebastian
My .mdp file looks like:
;
title = ttt
cpp = /lib/cpp
include = -I../top
constraints = hbonds
integrator = md
cutoff-scheme = verlet
;define = -DPOSRES ; for possition restraints
dt = 0.002 ; ps !
nsteps = 100000000 \
nstcomm = 25 ; frequency for center of mass
motion
removal
nstcalcenergy = 25
nstxout = 100000 ; frequency for writting the
trajectory
nstvout = 100000 ; frequency for writting the
velocity
nstfout = 100000 ; frequency to write forces to
output trajectory
nstlog = 10000 ; frequency to write the log file
nstenergy = 10000 ; frequency to write energies to
energy file
nstxtcout = 10000
xtc_grps = System
nstlist = 25 ; Frequency to update the neighbor
list
ns_type = grid ; Make a grid in the box and only
check atoms in neighboring grid cells when constructing a new neighbor
rlist = 1.4 ; cut-off distance for the
short-range neighbor list
coulombtype = PME ; Fast Particle-Mesh Ewald
electrostatics
rcoulomb = 1.4 ; cut-off distance for the coulomb
field
vdwtype = cut-off
rvdw = 1.4 ; cut-off distance for the vdw
field
fourierspacing = 0.12 ; The maximum grid spacing for the
FFT grid
pme_order = 6 ; Interpolation order for PME
optimize_fft = yes
pbc = xyz
Tcoupl = v-rescale
tc-grps = System
tau_t = 0.1
ref_t = 300
energygrps = Protein Non-Protein
Pcoupl = no;berendsen
tau_p = 0.1
compressibility = 4.5e-5
ref_p = 1.0
nstpcouple = 5
refcoord_scaling = all
Pcoupltype = isotropic
gen_vel = no;yes
gen_temp = 300
gen_seed = -1
Thanks a lot
Sebastian
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users>
<htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
* Please search the archive at http://www.gromacs.org/**
Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/**
Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>before
posting!
* Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read
http://www.gromacs.org/****Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists>
<http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
* Please search the archive at http://www.gromacs.org/**
Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before
posting!
* Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read
http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
