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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
