Sayan Bagchi wrote:
Hello All,
I was trying to run a MD simulation of a 17 amino acid peptide. At the
position restraint step, the program crashed after running ~536 ps.
It gave the error message:
"t=536.242 ps: Water molecule starting at atom 6101 cannot be settled.
Check for bad contacts and/or reduce the timestep. Wrote pdb files with
previous and current coordinates."
So I looked into the pdb files for atom 6101:
In the last but one step, the pdb file looks like:
ATOM 6101 OW SOL 1970 44.896 30.613 17.849 1.00 0.00
ATOM 6102 HW1 SOL 1970 45.375 30.296 18.668 1.00 0.00
ATOM 6103 HW2 SOL 1970 44.264 29.904 17.537 1.00 0.00
In the last step, the pdb file looks like:
ATOM 6101 OW SOL 1970
395154652137521152.000-290190255628222464.000695407981780533248.000
1.00 0.00
ATOM 6102 HW1 SOL 1970
-2104656020830683136.0005806908484133847040.000-6427192471385538560.000
1.00 0.00
ATOM 6103 HW2 SOL 1970
1131095442881249280.000593978790032441344.0001018902650772520960.000
1.00 0.00
So, there is clearly something wrong. What should I do now to solve this
problem?
http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-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
