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 <jalem...@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 > > 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. > -- Best Pavan Kumar
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