Dear Dr Roitberg,
Thanks for your answers.
My system is one of nodes (compute-0-2) in rocks system. But I just have
access to it and use for MD simulation, only.This node has 8 processors.
Unfortunately, I have remote connection to system and I have internet
problem and I can not access to files to Monday. Now is weekend in my
country.
I will check and visualize it.
In this case, in the info file,
NSTEP = 82500 TIME(PS) = 6665.000
I have another question. I have many protein-ligand complex to do MD
simulation.
In an another complex on another node of rocks (that I just have access to
it ), in the first production phase, I encountered with an interesting
point. sander was stopped. End of the out file is as follows:
NSTEP = 862500 TIME(PS) = 3225.000 TEMP(K) = 300.70 PRESS =
66.4
Etot = -91819.1456 EKtot = 23880.5373 EPtot =
-115699.6829
BOND = 991.8114 ANGLE = 2600.1910 DIHED =
3410.4648
1-4 NB = 1178.1472 1-4 EEL = 14041.4112 VDWAALS =
12746.1452
EELEC = -150667.8536 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 10042.1420 VIRIAL = 9489.3132 VOLUME =
385716.3526
Density =
1.0271
Ewald error estimate: 0.3641E-06
------------------------------------------------------------------------------
NSTEP = 865000 TIME(PS) = 3230.000 TEMP(K) = 301.75 PRESS =
57.9
Etot = -92106.4028 EKtot = 23964.1744 EPtot =
-116070.5772
BOND = 1005.2157 ANGLE = 2636.4786 DIHED =
3385.8516
1-4 NB = 1142.1352 1-4 EEL = 13988.7767 VDWAALS =
13041.7090
EELEC = -151270.7440 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 10141.9697 VIRIAL = 9659.8830 VOLUME =
385573.9303
Density =
1.0275
Ewald error estimate: 0.1193E-03
------------------------------------------------------------------------------
NSTEP = 867500 TIME(PS) = 3235.000 TEMP(K) = 301.48 PRESS
***************************************************************************************************
While end of the info file is as follows:
NSTEP = 2500000 TIME(PS) = 6500.000 TEMP(K) = 299.05 PRESS =
197.7
Etot = -92057.6812 EKtot = 23749.9389 EPtot =
-115807.6201
BOND = 970.4243 ANGLE = 2638.3735 DIHED =
3421.2260
1-4 NB = 1168.8488 1-4 EEL = 13997.9525 VDWAALS =
12941.0212
EELEC = -150945.4663 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 10058.1946 VIRIAL = 8412.3404 VOLUME =
385481.4470
Density =
1.0277
Ewald error estimate: 0.3833E-04
What is the reason of this issue? Have this md simulation ended?
Best,
Atila
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Oct 23 2015 - 08:30:03 PDT
