hi,
On Thursday 01 June 2006 21:43, Jorge Hernandez Fernandez wrote:
Dear GRMxers:
We need some help in running our Gromacs 3.2.1 parallel environment
in 5 nodes of SunFires V20v (dual-core Opteron 2.2, 4 GB DDR2 RAM), gigabit
eth, mpich-1.2.7, using Sun Grid Engine 6.0.
Update to
David Mobley wrote:
grompp (usual args) file.dat
grompp file.dat 21
Gianluca
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It is all about order.
You have to include the position restraint .itp directly after the
molecule .itp (or inside the molecule.itp).
If you place it behind the solvent .itp it will assume the position
restraints refers to the solvent.
The atom numbers in the position restraint should match
Hi all.
Of course I want SSE enabled. There is no sense in benching it against
different compilers if in one you enable the speed and on the other,
and in the other you remove almost every optimization. That's why in
the last message I've sent the eror I'm getting in the compilation:
If it is, just let me know, cause I'm tracking those down (finding a
script
way to back up original files before edition.) and at the same time trying
to find some sort of magical flag to convince icc to *not* use the
invsqrt function or the math.h file at all (second choice seems to
me a
Hi Bharat,
This is the same tutorial that led me astray when I first began trying free
energy
calculations in Gromacs. I am not sure how close to the experimental value the
author
intended to get with this hydration free energy tutorial. If you are using a
recent
version of Gromacs, be aware
From my browsing of list archives I can only recall seeing advice that
hyperthreading
cannot offer more Gromacs performance. For all I know this remains true if
you're trying
to use MPI to accelerate single calculations on hyperthreaded processors.
However, I
have discovered that it may be
Jianwei Wang wrote:
we use PME and our results (energy terms) seem depend on the charge group
assignment. Based on the manual, the results should not have anything to do
with charge groups. How can we turn off the charge groups.
Jianwei
___
Ok, I think I got it. Compiled. ;)
About a thousand tricks. I'll publish a tutorial later. But, basically:
1 - Change all invsrt calls to gmx_inv-sqrt (57 entries, 12 files);
2 - Edit the Makefile.in in the
nb_kernels directories, changing the line LTCCASCOMPILE = $(LIBTOOL)
--mode=compile
Debashis Dutta wrote:
Hi,
I am trying to estimate the dipole moment of zwitterionic form
of alanine in water using Gromacs and am looking for some suggestions on
the force field to use.
You're probably better off using quantum chemistry for this. Of course
you can run g_dipoles on a
Jones de Andrade wrote:
Ok, I think I got it. Compiled. ;)
About a thousand tricks. I'll publish a tutorial later. But, basically:
1 - Change all invsrt calls to gmx_inv-sqrt (57 entries, 12 files);
2 - Edit the Makefile.in http://Makefile.in in the nb_kernels
directories, changing the line
Jianwei Wang wrote:
we use PME and our results (energy terms) seem depend on the charge group
assignment. Based on the manual, the results should not have anything to do
with charge groups. How can we turn off the charge groups.
Jianwei
___
Dear all,
I am running the simulated annealing for a protein solvented in a water box,
but I get such LINCS WARNING as max 2022834176.00 (between atoms 5655 and 5658) rms 81089176.00
Why? Does it mean that my system is exploring?
The following is my mdp file and some of the LINCS
Hi gmx-users,
I am setting up a membrane inserted protein simulation.
The protein is mutated at a specific place and attached to a label and
this is inserted into the POPC membrane (434 lipids). The label is a
small molecule whose force field params were generated on PRODRG
server.
Everything
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