Em 05/04/2015 14:44, "Jashimuddin Ashraf" <jashimuddin.ashra...@gmail.com> escreveu: > > Dear gromacs users, > > I am trying to simulate liquid SO2 (Sulphur dioxide). So I tried to create > an equilibrated structure of SO2 molecules using the gmx insert-molecules > function. As I try to minimize the energy of the system, I always get this- > > ------------------------------------------------------------------------------------------------------------------------ > Energy minimization has stopped, but the forces have not converged to the > requested precision Fmax < 10 (which may not be possible for your system). > It > stopped because the algorithm tried to make a new step whose size was too > small, or there was no change in the energy since last step. Either way, we > regard the minimization as converged to within the available machine > precision, given your starting configuration and EM parameters.
That isn't necessarily a problem here, unless the maximum force is too high. You have requested a low threshold (emtol =10) and the machine precision can't reach it on simple precision. > ------------------------------------------------------------------------------------------------------------------------ > > I tried to analyze my .gro file that the gmx insert-molecules function is > returning me and found that some of my SO2 have a bond in between them. Is > this what causes the energy minimization to crash? Also, the .gro file just outputs atoms coordinates. There is no 'bonds' on it. Usualy, that is a visualization problem. Is there any way I can > prepare an equilibrated system of liquid SO2 ? Yes. Read the paper 'Force field benchmark for organic liquids' and you might get an idea how to do it. > > My SO2.itp file is like this (I made this an .itp because I wish to study > this system along with some other molecules)- > > ------------------------------------------------------------------------------------------------------------------------ > > [ moleculetype ] > ; Name nrexcl > SO2 3 > > [ atoms ] > ; nr type resnr residue atom cgnr charge mass > typeB chargeB massB > > 1 opls_202 1 SR S 1 0.6512 32.07 > ;qtot 0.6512 > 2 opls_326 1 SR O1 2 -0.3256 15.99940 > ;qtot 0.3256 > 3 opls_326 1 SR O2 3 -0.3256 15.99940 > ; qtot 0 > > > ; opls_202 S 16 32.07 0.6512 A 3.61500e-01 1.2125232 > ; opls_326 O 8 15.99940 -0.3256 A 3.00500e-01 0.47756176 > > [ bonds ] > ; ai aj funct c0 c1 c2 c3 > 1 2 1 0.1434 635968.0 > 1 3 1 0.1434 635968.0 > > [ distance_restraints ] > ; ai aj type index type' low up1 up2 fac > 1 2 1 0 1 1.149 1.490 1.490 1.0 > 1 3 1 0 1 1.149 1.490 1.490 1.0 > > [ angles ] > ; ai aj ak funct c0 c1 > c2 c3 > 2 1 3 1 119.5 1359.8 > ------------------------------------------------------------------------------------------------------------------------ > > I have also uploaded the .gro file that the gmx insert-molecules function > is returning me after this text. > > SO2_box300.gro > < https://docs.google.com/file/d/0B8p1k0KkNddyUEN3dzZRZE5keXM/edit?usp=drive_web > > > Thanks in advance. > -- > 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. -- 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.