Dear Amber Developers,
I am running H-REMD simulations of a peptide using the
CUDA version of Amber14. I had no problems running the
first 100 ns of the simulation, but when I tried to
restart it, the run aborted with the error message:
| ERROR: I could not understand line 14935
0.0061866 0.2322136 -0.1654300 0.5206336 0.6339461 0.2485021
Since in my system I have 29864 atoms and the restart file
shows the coordinates of two atoms per line, line 14935 is
the line where the velocities begin (considering also the
two lines before the coordinates). The program thus behaves
as if it doesn't understabd that it must perform a restart,
so I am wondering if there is some special instruction to
restart H-REMD.
Here is the content of my input file (for example file
hremd.mdin.001):
H-REMD
&cntrl
irest=1, ntx=5,
nstlim=1250, dt=0.002,
ntt=3, gamma_ln=1.0,
tempi=300.0, temp0=300.0,
ig=578,
ntc=2, ntf=2, nscm=1000,
ntp=0, ntb=1, cut=8.0,
ntpr=1250, ntwx=1250, ntwr=1250,
numexchg=40000,
/
The groupfile (hremd.groupfile) is:
-O -rem 3 -remlog rem_R2.log -i hremd.mdin.001 -o hremd_R2.mdout.001 -c
hremd_R1.rst.001 -r hremd_R2.rst.001 -x hremd_R2.mdcrd.001 -inf
hremd_R2.mdinfo.001 -p vdac2_wat_ions_1.0.prmtop
-O -rem 3 -remlog rem_R2.log -i hremd.mdin.002 -o hremd_R2.mdout.002 -c
hremd_R1.rst.002 -r hremd_R2.rst.002 -x hremd_R2.mdcrd.002 -inf
hremd_R2.mdinfo.002 -p vdac2_wat_ions_0.9.prmtop
and so on
Finally the program is launched with the following script:
#!/bin/bash
source /etc/modules.sh
module load intel openmpi amber14
export CUDA_VISIBLE_DEVICES=0,1,2,3
mpirun -np 8 pmemd.cuda.MPI -ng 8 -groupfile hremd.groupfile
Did I make any mistake or is there some special instruction
to restart H-REMD ?
Thank you very much for your help and kind regards,
Carlo Guardiani
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Dec 10 2014 - 02:00:02 PST
