Hi Gupta, :
Is there any problem with server or running on multiple thread.
your system seems to be very small and is probably subject
to strong fluctuations in pressure and/or energy. Could
you please create two directories containing (only) the
- mdp file for input (your md.mdp)
- topology
On 2/27/14, 8:32 AM, gupta.rakesh082 wrote:
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 convers
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
On 2/27/14, 2:16 AM, gupta.rakesh082 wrote:
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 -
Strange.
Sometimes things like this may happen if you incorrectly treat
periodicity between runs.
Without having the system at hand, I cannot say more.
Dr. Vitaly V. Chaban
On Thu, Feb 27, 2014 at 8:16 AM, gupta.rakesh082
wrote:
> EM RUN
>
> Steepest Descents converged to machine precision i
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
On 2/26/14, 10:50 AM, gupta.rakesh082 wrote:
I am using gromacs 4.6.5. Surprisingly system is stable at such high
potential energy. I created bilayer system using packmol then solvated it
with water using genbox.
I did energy minimization using following command
grompp -f em.mdp -c cerblayer.
I am using gromacs 4.6.5. Surprisingly system is stable at such high
potential energy. I created bilayer system using packmol then solvated it
with water using genbox.
I did energy minimization using following command
grompp -f em.mdp -c cerblayer.gro -p cer.itp -o min.tpr
mdrun -c -v -deffnm min
On 2/26/14, 12:51 AM, gupta.rakesh082 wrote:
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 (~
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
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