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.
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Oct 23 2016 - 02:30:02 PDT
