I find the structure of min.rst is odd. But what can I do ?
The structures see the attachment. I just pick out the ligands.
May be change the hydrogen site in ligand will work ?
在2016年10月22 15时42分, "Bill Ross"<ross.cgl.ucsf.edu>写道:
If you convert min.rst back to pdb and look at it, is anything odd? I
wonder if you have a bond through a ring or something. Note that in your
min.output, the atom with GMAX is
H13 13967
and before that it was nearby atom
O24 13965
I would look in that area of your pdb for clues.
Also you might try starting temp of 1K to see what happens.
Bill
On 10/22/16 12:21 AM, windy wrote:
> Hi, I test it in nstlim=100 under pmemd.MPI, it shows:
>
> vlimit exceeded for step 0; vmax = **********
> vlimit exceeded for step 1; vmax = 20.9314
> vlimit exceeded for step 3; vmax = **********
> vlimit exceeded for step 3; vmax = **********
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 3
>
>
> It may caused by the large rate in the min.rst? So I may think it really the problems of the min step.
>
> By the way, other prmtop can run smoothly under the same parameter and also I remove the ligand, it can run rightly.
>
> What's the problem of my ligand? I really be puzzled.
>
>
>
>
>
>
> 在2016年10月22 14时26分, "Bill Ross"<ross.cgl.ucsf.edu>写道:
>
> Error: unspecified launch failure launching kernel kNLSkinTest
> cudaFree GpuBuffer::Deallocate failed unspecified launch failure
>
> http://archive.ambermd.org/201506/0288.html
>
> On 10/21/16 11:09 PM, windy wrote:
>> 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.
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
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Received on Sat Oct 22 2016 - 02:30:02 PDT
