[gmx-users] Adding TPO and SEP to G53a6 Forcefield

Pavan Kumar kumar.pavan006 at gmail.com
Tue Mar 4 12:56:52 CET 2014


Hello Users,
I am running mdrun for nsteps = 10000000 ; 20 ns.
Even though i have enough space on my cluster around 17 GB, I am getting
the following error.
*Cannot fsync 'md1.log'; maybe you are out of disk space?*
What could be the reason for such errors. I am attaching my mdp file.
Thanks in Advance.


On Wed, Feb 26, 2014 at 6:21 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/26/14, 7:05 AM, lalithkumar wrote:
>
>> Dear Dr. Justin,
>>
>> Thank you for pointing out the details of error. I have missed out the
>> version of GROMACS I have been using and so I would like to let you know
>> that my version is 4.5.7. In this version ffnonbonded.itp file of the
>> gromos53a6.ff forcefield doesnt have pairtypes fr LJ-14 interactions. I
>>
>
> I doubt that's correct; every Gromacs version I've ever had contained
> [pairtypes] in this file.  Check again.  I don't have 4.5.7 installed
> anywhere, but in 4.6.x (several versions), it is clearly present.
>
>
>  should agree that I dont know how they can be generated and to specify
>> manually. So, in a crude way I can say that I have copied all the LJ 14
>> types from the ffG43a1p forcefield at the gromacs contributors link:
>> http://www.gromacs.org/Downloads/User_contributions/Force_fields
>>
>> This includes the following addition lines:
>>
>> ; begin insert from pamac_hsnnb.itp
>> ; [ pairtypes ]
>> ; for LJ 14 - use same for OP as for OA
>>        OP        O  1  0.0022619536  9.687375e-07
>>        OP       OM  1  0.0022619536  9.687375e-07
>>        OP       OP  1  0.0022619536  1.265625e-06
>>        OW       OP  1  0.0024331696   1.737e-06
>>         N       OP  1  0.0023475616  1.463625e-06
>>        NT       OP  1  0.0023475616  1.463625e-06
>>        NL       OP  1  0.0023475616  1.463625e-06
>>        NR       OP  1  0.0023475616  1.463625e-06
>>        NZ       OP  1  0.0023475616  1.463625e-06
>>        NE       OP  1  0.0023475616  1.463625e-06
>>         C       OP  1  0.0023009528  2.066625e-06
>>       CH1       OP  1  0.0025663376  2.174625e-06
>>       CH2       OP  1  0.0032687988  3.000375e-06
>>       CH3       OP  1  0.0039370168  3.907125e-06
>>       CH4       OP  1  0.005459888  6.59475e-06
>>       CR1       OP  1  0.003536086  3.24675e-06
>>        HC       OP  1  0.000437552  1.38375e-07
>>         H       OP  1           0           0
>>       DUM       OP  1           0           0
>>         S       OP  1  0.0047521952   4.068e-06
>>      CU1+       OP  1  0.000972602  8.053875e-08
>>      CU2+       OP  1  0.000972602  8.053875e-08
>>        FE       OP  1           0           0
>>      ZN2+       OP  1  0.000972602  1.09305e-07
>>      MG2+       OP  1  0.0003842848  6.56775e-08
>>      CA2+       OP  1  0.001507652  7.939125e-07
>>         P       OP  1  0.005773784  5.299875e-06
>>        AR       OP  1  0.003764374  3.53025e-06
>>         F       OP  1  0.0016322592  9.81225e-07
>>        CL       OP  1  0.0044525672  4.399875e-06
>>        BR       OP  1  0.0016332104  9.1035e-06
>>      CMET       OP  1  0.0044806276  5.1373125e-06
>>      OMET       OP  1  0.0022619536  1.265625e-06
>>       NA+       OP  1  0.00040373684  1.63125e-07
>>       CL-       OP  1   0.0055883  1.16325e-05
>>      CCHL       OP  1  0.0024394475   2.268e-06
>>     CLCHL       OP  1  0.004334666 4.1738625e-06
>>      HCHL       OP  1  0.0002920184  7.377075e-08
>>     SDMSO       OP  1  0.0048877412 5.216175e-06
>>     CDMSO       OP  1  0.0045248108  5.2475625e-06
>>     ODMSO       OP  1  0.0022663291  9.752175e-07
>>      CCL4       OP  1  0.0024394475  3.1014e-06
>>     CLCL4       OP  1  0.0041472796  4.01985e-06
>>        SI       OP  1           0           0
>> ; end insert from pamac_hsnnb.itp
>>
>> And I had copied them as is to my ffnonbonded.itp file in modified
>> gromos53a6.ff folder. Also, I have also modified atomtypes as per latest
>> versions (for example CMET to CMet).
>>
>> Finally, I could pass the grompp set now and can run mdrun too
>> successfully.
>> Now I need your valuable review to know whether I had done is correct or
>> can
>> I do better than this way. If so please suggest some helping material
>> regarding process of setting user defined LJ 14 pair types interactions to
>> gromos53a6ff or any forcefield. And also, briefly comment on how
>> difference
>> with my results by doing in the method mentioned by me and with any other
>> suggested method from your side.
>>
>> Please let me know if any further information to be provided from my side
>>
>>
> What you've done is not correct.  You've made a mixed force field that is
> not necessarily viable.  You need proper parameters within a single force
> field, not borrowed from some other parameter set, unless you can
> demonstrate through rigorous testing and validation that what you've done
> is correct.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
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-- 
Best
Pavan Kumar


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