[gmx-users] Error with tabulated potential and tip4p water model
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.
Re: [gmx-users] Error with tabulated potential and tip4p water model
Immediately, or after some EM steps? Mark On Sun, Aug 3, 2014 at 12:56 PM, Udaya Dahal 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.
Re: [gmx-users] Error with tabulated potential and tip4p water model
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 wrote: > Immediately, or after some EM steps? > > Mark > > > On Sun, Aug 3, 2014 at 12:56 PM, Udaya Dahal > 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.
Re: [gmx-users] Error with tabulated potential and tip4p water model
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 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 > wrote: > > > Immediately, or after some EM steps? > > > > Mark > > > > > > On Sun, Aug 3, 2014 at 12:56 PM, Udaya Dahal > > 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.
Re: [gmx-users] Error with tabulated potential and tip4p water model
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 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 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 > > wrote: > > > > > Immediately, or after some EM steps? > > > > > > Mark > > > > > > > > > On Sun, Aug 3, 2014 at 12:56 PM, Udaya Dahal > > > 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.g
