Hi Peter, Sorry for the delay. According to your suggestion, I have equilibrated my system with gradually increasing time step (1, 2, 5, 10, 15, 20 fs). After that, the production step is running successfully.
Thanks a lot for your kind help! Best regards, Sudip On Thu, Jun 29, 2017 at 2:32 PM, Peter Kroon <[email protected]> wrote: > Hi Sudip, > > > we had a short discussion over coffee. We also get these warnings, but > they don't generally lead to significant instabilities. This means you > probably have an equilibration issue. Could you try equilibrating your > system with increasing timesteps? So first equilibrate with 5fs, then > continue with 10 fs, 15fs and finally 20 fs. > > If that doesn't work, could you give a more detailed description of your > system? > > > Peter > > > On 29-06-17 10:07, Peter Kroon wrote: > > Hi Sudip, > > > > > > there's a dedicated forum for these Martini questions on cgmartini.nl. > > Recently there was a similar question there > > (http://cgmartini.nl/index.php/component/kunena/7-mdp- > options/5491-gpu-verlet-oscillational-period#7308). > > > > To summarize, the bonds between the backbone beads are extremely stiff. > > If your protein is small/short enough you can change them to > > constraints. I'll start a discussion in the group here on how to handle > > it further. > > > > > > Peter > > > > > > On 29-06-17 09:06, Sudip Das wrote: > >> Dear All, > >> > >> I am running a CGMD simulation of protein and surfactant in water with > >> Martini2.0 force field for surfactant and water and ELNEDYN2.2 force > field > >> for protein. > >> > >> The system is running fine with 20 fs integration timestep. But it > leads to > >> solid phase of water. So, I have introduce antifreeze water beads (which > >> are 10% in number w.r.t. the total number of water beads). But after > this, > >> simulation is not at all running with 20 fs timestep and gives the > error: > >> > >> segmentation fault (signal 11) > >> > >> Within output file, it shows: > >> > >> Step 2, time 0.04 (ps) LINCS WARNING > >> relative constraint deviation after LINCS: > >> rms 0.007237, max 0.028381 (between atoms 20 and 21) > >> bonds that rotated more than 30 degrees: > >> atom 1 atom 2 angle previous, current, constraint length > >> 20 21 30.4 0.1981 0.1895 0.1950 > >> > >> > >> I have tried to solve it in several ways, i.e., decreasing the time > steps > >> (it is running fine with 2 fs), equilibrating the system properly, > >> compiling and running in serial version of gromacs (to test whether the > >> error comes due to domain decomposition during parallel run) etc. Even > >> though, I am getting the same error. > >> > >> While compiling the job with grompp, I got the below warning: > >> > >> WARNING 1 [file system.top, line 18]: > >> The bond in molecule-type Protein_A between atoms 1 BB and 2 BB has an > >> estimated oscillational period of 9.7e-02 ps, which is less than 5 > times > >> the time step of 2.0e-02 ps. > >> Maybe you forgot to change the constraints mdp option. > >> > >> But, following the link > >> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx- > users/2014-May/089120.html > >> , I have ignored this warning using -maxwarn flag. Probably this > wouldn't > >> be the cause for this error, as I got exactly the same warning for the > >> system without antifreeze water beads. > >> > >> > >> Please help me to solve this problem. I would be happy to share my > files if > >> needed. > >> > >> Thanks in advance! > >> > >> Best regards. > >> Sudip > > > > > > -- > 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 [email protected]. > -- 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 [email protected].
