Im not sure on the prices of these systems any more, they are getting dated
so they will be on the low end price wise. I have a 30,000 ish atom lipid
system for all my simulations so this might be helpful:
System 1
CPU - dual 6 core xeon @ 2.8 GHz
GPU - 2x GTX 680
50 ns/day
System 2
CPU - dual 4
Hello Nilesh,
it sounds like you have a similar problem to mine, except my original run
has large energy fluctuations and the rerun does not. By chance is your
gromacs version installed with mpi on? i think i have narrowed my problem to
a bug in the installation with mpi.
If you search for my
I can confirm this, I have noticed this as well.
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FYI I have done some more experimenting on the problem with different
versions and computers running the exact same start .tpr file and this is
what ive found:
Computer A with 4.6.1 or 4.6.3 with MPI = random energy drops
Computer A with 4.6.1 or 4.6.3 without MPI = no random energy drops
I have just successfully installed 4.6.3 using Intel compilers this morning
with the following:
Intel 12.1.3
cuda 5.0.35
openmpi 1.6.2
cmake 2.8.10.2
FFTW 3.3.3
I did not use gcc at all. (intel/12.1.3/icc/bin/icc for CUDA_HOST_COMPILER)
Hope it helps,
Brad
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If i understand the problem correctly, you can plot the com of any group of
atoms as a function of time with g_traj. Create an index file of whatever
atoms you want using make_ndx then use g_traj with -com flag to plot com of
the group.
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I used the mdrun -rerun option to recalculate the energies of the system and
it gave me nearly the same energy plot but without the random drops(see plot
below). I am still unsure what is causing the jumps but i do not believe it
is from my system. Since the energy is used in the calculation for
This was done on v 4.6.1
md50.mdp:
title= MD simulation
integrator = md ; MD integrator
tinit= 0
dt = 0.002; 2 fs timestep
nsteps = 5000 ; Number of
To be honest, i have not updated that box to the newest version. If it
appears to be a serious bug i could do it and rerun these sims to see if it
does persist.
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Hello,
I am performing a MD simulation on a small molecule in a bilayer. The
simulation seems to run smoothly but when i graph the energy i see large
changes in energy randomly throughout the run(see graph).
http://gromacs.5086.x6.nabble.com/file/n5010260/potential_12cc50.png
I have looked at
looking at the first 2 peaks, they are created from single outlying points in
the trajectory. Visually, I can see no discernible difference between it and
the frame before/after with the higher energy.
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i find the trjconv option -center skips random frames(less then 1 % of
frames), and by random frames i mean that these frames are not equally
spaced apart in time. I have tried -center and -center -boxcenter zero
flags but both produce the same problem.
Does anyone know a fix/workaround?
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The trajectory file is from a consecutive run so i would hope the frames are
evenly spaced.
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Checking file md50.xtc
Reading frame 0 time0.000
# Atoms 27392
Precision 0.001 (nm)
Last frame 5 time 10.000
Item#frames Timestep (ps)
Step 500012
Time 500012
Lambda 0
Coords 500012
Velocities 0
Forces
Ahh, yes perhaps i was unclear. The output file also has the same number of
steps.
Checking file md50_centered.xtc
Reading frame 0 time0.000
# Atoms 27392
Precision 0.001 (nm)
Last frame 5 time 10.000
Item#frames Timestep (ps)
Step 500012
Time
ahh, i thought that the program was skipping as in not doing the centering
command on certain frames due to one reason or another. Ill look into your
suggestion
Thank you very much for the help.
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Hello,I have had the same problem with CHARMM-GUI however I have found a
decent work-around procedure: 1. Go to your input .gro file and locate the
atom with infinite force (atom 23533 in this case)2. Change one of the x,y,z
positions of that atom by about /- 0.5.3. Rerun grompp with the new
I have been lost in the sea of terminology for installing gromacs with
multi-processors. The plan is to upgrade from 4.5.5 to the 4.6 and i
want the optimal install for my system. There is a a nice explanaion at
http://www.gromacs.org/Documentation/Acceleration_and_parallelization
but the
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