Dear justin Thank you for your previous reply I am running NPT Equlibration at 20 ps with dt 0.0002 in 100000 steps Without usage of Lincs Algorithm and its related parameters it runs Successfully . But When I Increase dt from 0.0002 to 0.002 then I have got error as follows in grompp
WARNING 1 [file 2KDQTR.top, line 71]: The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H1 has an estimated oscillational period of 1.0e-02 ps, which is less than 5 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. Then I have used the Lincs Algorithm and its related parameter Then I have got Error during Mdrun as follows I saw there Are Plenty Of discussion in Mailing list But I am Not Able to come to conclusion relative constraint deviation after LINCS: rms 0.015272, max 0.577865 (between atoms 120 and 122) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Wrote pdb files with previous and current coordinates 129 131 39.1 0.1475 0.1664 0.1330 129 130 37.8 0.1191 0.1243 0.1230 125 126 38.5 0.1738 0.1508 0.1530 124 129 103.2 0.0962 0.9157 0.1530 124 125 124.3 0.1725 0.8648 0.1530 122 124 169.9 0.4717 2.5621 0.1470 122 123 168.0 0.2655 3.1890 0.1000 120 122 176.3 0.5957 7.3414 0.1330 120 121 172.8 0.5550 6.4843 0.1230 What does the Above Fact Indicates I mean the Problem is in Topology or in MD Parameter file ? With Regards S.Vidhyasankar -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
