[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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