Dear amber users
I was running the second prod step. Unfortunately, due to power failure,
sander was stopped.
My prod.in file is as follows:
&cntrl
imin=0,irest=1,ntx=5,
nstlim=2500000,dt=0.002,
cut=10.0,ntb=2,ntp=1,taup=2.0,
ntc=2,ntf=2,
ntpr=2500,ntwx=2500,
ntt=3,gamma_ln=2.0,
temp0=300.0,
/
I have to have a trajectory containing 5000 ps and 1000 frames.
After power failure, the end of the prod2.out file is as follows:
.
.
.
.
------------------------------------------------------------------------------
NSTEP = 2445000 TIME(PS) = 11390.000 TEMP(K) = 299.92 PRESS =
-23.9
Etot = -92384.3446 EKtot = 23793.4048 EPtot =
-116177.7494
BOND = 987.7799 ANGLE = 2608.5156 DIHED =
3411.8147
1-4 NB = 1154.3951 1-4 EEL = 14108.7303 VDWAALS =
13059.2879
EELEC = -151508.2729 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 10071.6907 VIRIAL = 10270.6229 VOLUME =
385008.3181
Density =
1.0277
Ewald error estimate: 0.1991E-03
------------------------------------------------------------------------------
To continue, I made new.in file, as follows: (nstlim =
2500000-2445000=55000)
prod complex_solvated
&cntrl
imin=0,irest=1,ntx=5,
nstlim=55000,dt=0.002,
cut=10.0,ntb=2,ntp=1,taup=2.0,
ntc=2,ntf=2,
ntpr=2500,ntwx=2500,
ntt=3,gamma_ln=2.0,
temp0=300.0,
/
After completing run, I concatenated 2 mdcrd files using cpptraj.
I saw mixed.mdcrd trajectory using vmd. In vmd, there are 999 frames
instead of 1000.
Why? Is my manner wrong?
Any help will highly appreciated.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Nov 06 2015 - 06:00:04 PST
