Thank you mark for the reply. But here i have only one polymer which i used optimized structure polymer and used genbox to generate box of solvent which obviously puts the water at different lattice points. It was never a problem to simulate when I was using the LJ potential. So, my concern here is about how the gromacs reads the table internally.
So far, in the table, what I did is; I made all f,f',h,h' columns zero and calculated the total (sum of electrostatics+LJ/Buckingham+user defined potential) potential and put in the column g and the negative derivative of g in g' column thereby putting all the coefficients as 1 in the .itp file. When I try to use that table it gives me the warning that the derivative(-force) deviates from the potential by 164%(one example). While reading the Manual, I found that it uses the Cubic splines Algorithm to regenerate the table internally. I am not sure if that algorithm was not compatible with the way i created the table(for potential) or it is something else. Looks like I am lost somewhere in between here because EM was never a great problem until I used the tabulated potential. Udaya On Tue, Aug 5, 2014 at 10:38 AM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Generating a sane starting structure is not really in GROMACS problem > space. You should take steps to ensure atoms are not closer to each other > than is physically reasonable, and probably start with the coordinates of > each molecule whole with respect to PBC. Start with a single polymer > solvated, then perhaps use genconf to add complexity. > > Mark > > > On Mon, Aug 4, 2014 at 8:48 AM, Udaya Dahal <dahal.ud...@gmail.com> wrote: > > > It was immediate. But I figured out the way to solve that issue. Looks > > like the starting initial configuration was not so good. A different > > starting structure at least gave me the energy minimization to few steps > > but I kind of really find very hard to have the energy minimized to > smaller > > value. The maximum force on the particular atom is around ...+03. Do I > > really have to amend each and every atom step by step(which still doesn't > > solve the problem) or there is any other specific way that we can get > > more/less energy minimized structure. Thank you for your help. > > > > > > On Sun, Aug 3, 2014 at 9:23 PM, Mark Abraham <mark.j.abra...@gmail.com> > > wrote: > > > > > Immediately, or after some EM steps? > > > > > > Mark > > > > > > > > > On Sun, Aug 3, 2014 at 12:56 PM, Udaya Dahal <dahal.ud...@gmail.com> > > > wrote: > > > > > > > I have tabulated potential for all the possible combinations(non > > > bonded). > > > > I am using Tip4p water model for the polymer water interaction. While > > > > running the energy minimization i got the error like below. > > > > > > > > Fatal error: > > > > Settle block crossing node boundaries > > > > constraint between atoms 664, 665, 666) > > > > For more information and tips for troubleshooting, please check the > > > GROMACS > > > > website at http://www.gromacs.org/Documentation/Errors > > > > > > > > Any idea to slove this issue.? > > > > > > > > Thank you, > > > > Udaya. > > > > -- > > > > 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. > > > > > > > > > > > -- > > Udaya Dahal, > > Graduate Assistant, > > Department of Physics, > > University of Connecticut > > -- > > 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. > -- 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.