By 'terminal H' I mean the H's that are on your phosphate groups or
whatever they are.
Hopefully someone with personal experience of this situation will chime in.
Bill
On 10/23/16 2:03 AM, windy wrote:
> I am a little understand what you meaning.
>
> I find so little resource about how to stiff the termial hydrogen by using the key words "amer atom fuse", "amber stiff hydrogen"
>
> But I cannot find some step by step methods on amber archive... Or just I cannot understand what they do ...
> Like this paper: MD simulations of hydrogen diffusion in ZIF-11 with a force field fitted to experimental adsorption data
>
> It is a hard problem to me and I maybe remove the ligand ...
>
> Thanks for your patient answer .
>
> Chen.
>
>
>
>
>
> 在2016年10月23 07时14分, "Bill Ross"<ross.cgl.ucsf.edu>写道:
>
> I am a bit out of my depth here, in that the number of P and O atoms
> indicates some interesting charge problems that don't often arise (30 of
> 48 atoms are P's or O's). I've only seen isolated cases like this
> before, not a whole ring-full of them, and never had to solve one for
> myself. I'm guessing you'll need to play with angles and torsions around
> those terminal H's to keep things stiff enough to not fuse. You might
> find something useful in the archives from those simpler cases
> (involving P, some possibly S). I wonder how much neighboring ring
> elements interact.
>
> Bill
>
> On 10/22/16 2:03 AM, windy wrote:
>> 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 Sun Oct 23 2016 - 10:30:02 PDT
