Hi, everyone,
I had a protein with ligands. When I put it into MD, it reported in heat step:
Error: unspecified launch failure launching kernel kNLSkinTest
cudaFree GpuBuffer::Deallocate failed unspecified launch failure
I first see the 'RESTARTED DUE to LINMIN FAILURE' in min.out, So I followed the tips in the following link:
http://structbio.vanderbilt.edu/archives/amber-archive/2008/1340.php
I change the "imin=1,maxcyc=10000,ncyc=1000, " to " imin=1,maxcyc=22000,ncyc=12000,"， But the 'RESTARTED DUE to LINMIN FAILURE' happened too (as follow):
NSTEP ENERGY RMS GMAX NAME NUMBER
11850 -5.5996E+05 1.7727E+04 8.3886E+06 O24 13965
BOND = 30484.6520 ANGLE = 2193.6343 DIHED = 8605.7828
VDWAALS = 43827.3652 EEL = -641883.3917 HBOND = 0.0000
1-4 VDW = 3102.4665 1-4 EEL = -6294.4058 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
11900 -5.5994E+05 1.7727E+04 8.3886E+06 O24 13965
BOND = 30484.6520 ANGLE = 2193.6344 DIHED = 8605.7828
VDWAALS = 43827.3652 EEL = -641883.3914 HBOND = 0.0000
1-4 VDW = 3102.4665 1-4 EEL = -6269.8014 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
11950 -5.5993E+05 1.7725E+04 8.3873E+06 H13 13967
BOND = 30484.6520 ANGLE = 2193.6345 DIHED = 8605.7828
VDWAALS = 43827.3652 EEL = -641883.3880 HBOND = 0.0000
1-4 VDW = 3102.4665 1-4 EEL = -6255.8578 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
12000 -5.5992E+05 1.7722E+04 8.3863E+06 H13 13967
BOND = 30484.6520 ANGLE = 2193.6345 DIHED = 8605.7828
VDWAALS = 43827.3652 EEL = -641883.3912 HBOND = 0.0000
1-4 VDW = 3102.4665 1-4 EEL = -6254.0335 RESTRAINT = 0.0000
.... RESTARTED DUE TO LINMIN FAILURE ...
.... RESTARTED DUE TO LINMIN FAILURE ...
I noticed that in some reply: "the RESTARTED DUE TO LINMIN FAILURE" can be ignored and I find the min.rst seems no error.
So I continue the heat by using this min.rst. And the error as follows:
Error: unspecified launch failure launching kernel kNLSkinTest
cudaFree GpuBuffer::Deallocate failed unspecified launch failure
So which is the key problems in my MD?
1. To change the force field parameter of ligands? The force field of ligands is generated in antechamber, it seems no errors (as attachment).
2. Change the min.in ? How to change? Anyone have ideas?
3. change the heat.in ? How to change?
Thanks for you reply.
Chen.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
- application/octet-stream attachment: IHP.prepi
Received on Fri Oct 21 2016 - 23:30:03 PDT
