Re: [gmx-users] Structural features for LINCS application
Il 16/03/2012 01:38, Mark Abraham ha scritto: On 16/03/2012 6:02 AM, Francesco Oteri wrote: Dear gromacs users, I am trying to simulate a protein (containing FeS cluster and a complex metal active site) using virtual site. I've to face a problem with LINCS. In particular, if I constrain only h-bonds without using virtual site, simulation runs fine but constraining all-bonds, simulation crashes after a lot of LINCS warning like: Step 356, time 0.712 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.408533, max 8.159325 (between atoms 2750 and 2754) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2750 2754 90.00.1365 1.2502 0.1365 In both cases simulation conditions are the same. The bonds causing problem belongs to the active site. I am wondering if there are structural features imparing the use of all-bonds constraints in LINCS. A second question is, how can I run MD with virtual site without all-bonds options. Coupled constraints, such as you might have in a cluster, can be delicate. Equilibrating with a quite small time step can be necessary. Mark Hi Mark, I've run 100ps at 0.5fs, and 1fs...but when I switch to 2fs it crashes. I've read in the manual and it seem that triangular structures might introduce problem, but I dont have such a structure in my protein. So, there are other coupled constraint that may cause problem in LINCS? Is it possible that the force constants can cause problem? Or anyway, is it possible using virtual site constraining only h-bonds? Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Structural features for LINCS application
Dear gromacs users, I am trying to simulate a protein (containing FeS cluster and a complex metal active site) using virtual site. I've to face a problem with LINCS. In particular, if I constrain only h-bonds without using virtual site, simulation runs fine but constraining all-bonds, simulation crashes after a lot of LINCS warning like: Step 356, time 0.712 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.408533, max 8.159325 (between atoms 2750 and 2754) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2750 2754 90.00.1365 1.2502 0.1365 In both cases simulation conditions are the same. The bonds causing problem belongs to the active site. I am wondering if there are structural features imparing the use of all-bonds constraints in LINCS. A second question is, how can I run MD with virtual site without all-bonds options. Thank you, Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Structural features for LINCS application
On 16/03/2012 6:02 AM, Francesco Oteri wrote: Dear gromacs users, I am trying to simulate a protein (containing FeS cluster and a complex metal active site) using virtual site. I've to face a problem with LINCS. In particular, if I constrain only h-bonds without using virtual site, simulation runs fine but constraining all-bonds, simulation crashes after a lot of LINCS warning like: Step 356, time 0.712 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.408533, max 8.159325 (between atoms 2750 and 2754) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2750 2754 90.00.1365 1.2502 0.1365 In both cases simulation conditions are the same. The bonds causing problem belongs to the active site. I am wondering if there are structural features imparing the use of all-bonds constraints in LINCS. A second question is, how can I run MD with virtual site without all-bonds options. Coupled constraints, such as you might have in a cluster, can be delicate. Equilibrating with a quite small time step can be necessary. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
