HI everyone,
I want to make a test using tables potential, I choose full-atoms benzene
molecules for example.firstly ,I transform the 12-6 LJ potential into table
potential, but when mdrun step, I got a error message as follows:
******************************************************************
Getting Loaded...
Reading file ben_md.tpr, VERSION 3.3.3 (single precision)
-----------------------------------------------------------------------------
One of the processes started by mpirun has exited with a nonzero exit
code. This typically indicates that the process finished in error.
If your process did not finish in error, be sure to include a "return
0" or "exit(0)" in your C code before exiting the application.
PID 16534 failed on node n0 (127.0.0.1) due to signal 11.
-----------------------------------------------------------------------------
**************************************************************************
here is my itp and table potential file:
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 1 no 1.0 1.0
[ atomtypes ]
; type mass charge ptype c6 c12
BEN 12 0 A 1.00 0.0000
[ moleculetype ]
; Name nrexcl
BEN 6
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 BEN 1 BEN C1 1 0 12.0110
2 BEN 1 BEN C2 2 0 12.0110
3 BEN 1 BEN C3 3 0 12.0110
4 BEN 1 BEN C4 4 0 12.0110
5 BEN 1 BEN C5 5 0 12.0110
6 BEN 1 BEN C6 6 0 12.0110
[ bonds ]
; ai aj fu c0, c1, ...
1 2 2 0.139 10800000.0 0.139 10800000.0 ; CAA CAB
2 3 2 0.139 10800000.0 0.139 10800000.0 ; CAA CAD
3 4 2 0.139 10800000.0 0.139 10800000.0 ; CAB CAC
4 5 2 0.139 10800000.0 0.139 10800000.0 ; CAC CAF
5 6 2 0.139 10800000.0 0.139 10800000.0 ; CAF CAE
6 1 2 0.139 10800000.0 0.139 10800000.0 ; CAE CAD
[ angles ]
; ai aj ak fu c0, c1, ...
1 2 3 2 120.0 505.0 120.0 505.0 ; HAA CAA CAB
2 3 4 2 120.0 505.0 120.0 505.0 ; HAA CAA CAD
3 4 5 2 120.0 505.0 120.0 505.0 ; CAB CAA CAD
4 5 6 2 120.0 505.0 120.0 505.0 ; CAA CAB HAB
5 6 1 2 120.0 505.0 120.0 505.0 ; CAA CAB CAC
6 1 2 2 120.0 505.0 120.0 505.0 ; HAB CAB CAC
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
1 2 3 4 2 0.0 167.4 0.0 167.4 ; imp CAA CAD CAB
HAA
2 3 4 5 2 0.0 167.4 0.0 167.4 ; imp CAB CAA CAC
HAB
3 4 5 6 2 0.0 167.4 0.0 167.4 ; imp CAC CAB CAF
HAC
4 5 6 1 2 0.0 167.4 0.0 167.4 ; imp CAF CAC CAE
HAF
5 6 1 2 2 0.0 167.4 0.0 167.4 ; imp CAE CAF CAD
HAE
6 1 2 3 2 0.0 167.4 0.0 167.4 ; imp CAD CAA CAE
HAD
part of table potential as follows:
0.36 0 0 0.65757 0 0 0
0.362 0 0 0.53518 0 0 0
0.364 0 0 0.42386 0 0 0
0.366 0 0 0.32271 0 0 0
0.368 0 0 0.23088 0 0 0
0.37 0 0 0.14758 0 0 0
0.372 0 0 0.07213 0 0 0
0.374 0 0 0.00385 0 0 0
0.376 0 0 -0.05783 0 0 0
0.378 0 0 -0.11347 0 0 0
0.38 0 0 -0.16358 0 0 0
0.382 0 0 -0.2086 0 0 0
0.384 0 0 -0.24897 0 0 0
0.386 0 0 -0.28507 0 0 0
0.388 0 0 -0.31727 0 0 0
0.39 0 0 -0.34588 0 0 0
0.392 0 0 -0.37121 0 0 0
0.394 0 0 -0.39354 0 0 0
0.396 0 0 -0.41312 0 0 0
0.398 0 0 -0.43018 0 0 0
0.4 0 0 -0.44495 0 0 0
*****************************
then ,I change somethings in itp files, add a new type C3,but set its
parameters the same as BEN, then em, md ,this time, it words well,but the
density of system are 10% less than the full-atom simulation with LJ12-6
potential. I want to know why? table potential can't give the accurate results?
another quetion is that, when using tables, if the system has only one type of
atoms, Gromas can't work well?
changes as follows:
********************************
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 1 no 1.0 1.0
[ atomtypes ]
; type mass charge ptype c6 c12
BEN 12 0 A 1.00 0.0000
C3 12 0 A 1.00 0.0000
[ nonbond_params ]
; i j func c6 c12
BEN C3 1 1.00 0.0000
[ moleculetype ]
; Name nrexcl
BEN 6
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 BEN 1 BEN C1 1 0 12.0110
2 BEN 1 BEN C2 2 0 12.0110
3 BEN 1 BEN C3 3 0 12.0110
4 C3 1 C3 C4 4 0 12.0110
5 C3 1 C3 C5 5 0 12.0110
6 C3 1 C3 C6 6 0 12.0110
*************************
table_BEN_BEN.xvg,table_BEN_C3.xvg,table_BEN_C3.xvg are all the same.
Best!
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