thanx Dr. Vitaly
could you please explain me what did you mean by incorrectly treating of
periodicity? Is it related to update of neighbour list? My system is
periodic in 3 dimension and pressure coupling is anisotropic.
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Hi Justin
The bilayer is full solvated. It has 128 ceramide and 5120 water molecules
(40 water molecule per ceramide).
I ran same simulation on my desktop machine it is working properly,
properties such as potential energy and area per lipid converse very nicely.
Is there any problem with ser
EM RUN
Steepest Descents converged to machine precision in 2820 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -2.9268122e+05
Maximum force = 1.9479546e+02 on atom 123
Norm of force = 6.3931437e+00
grompp -f em.mdp -c cerblayer.gro -p cer.itp -o min.tpr
mdrun -c -
EM RUNSteepest Descents converged to machine precision in 2820 steps,but did
not reach the requested Fmax < 10.Potential Energy = -2.9268122e+05Maximum
force = 1.9479546e+02 on atom 123Norm of force =
6.3931437e+00grompp -f em.mdp -c cerblayer.gro -p cer.itp -o min.tprmdrun -c
-v -deffnm
energy minimization and NPT MD run.
On Wed, Feb 26, 2014 at 4:41 PM, Justin Lemkul [via GROMACS] <
ml-node+s5086n5014819...@n6.nabble.com> wrote:
>
>
> On 2/26/14, 12:51 AM, gupta.rakesh082 wrote:
> > Dear allI performed MD simulation of lipid bilayer on my desktop it is
Dear allI performed MD simulation of lipid bilayer on my desktop it is giving
correct results and negative potential energy (~ -10^5) but when I ran the
same simulation on a server using multi thread (-nt 8), It is giving
positive potential energy (~ 10^5). Initially I thought it might be problem
w
