neeru sharma wrote:
Dear Gromacs users,
I have to simulate a system consisting of Protein+MG+GDP where Protein
is in complex with MG and GDP. I generated the GDP parameters using
antechamber and then converted the topology,coordinate and parameter
files to the corresponding gromacs format.
Then, I tried to start with the simulation using AMBER ff03 forcefield.
The system ran well till energy minimization step, but at equilibration
steps it is showing lincs error at NVT equilibration step.
What was the output of energy minimization? What I'm looking for is the actual
screen output with Epot and Fmax. Just because EM "completed" does not mean it
was necessarily sufficient.
I used 2 coupling groups for my system with lincs constraint algorithm
as follows:
*tc-grps = Protein_MG_GDP Water_and_ions *
I tried turning off lincs warning too, den NVT equilibration was done
finely but the system was blowing up during NPT equilibration. I tried
No, NVT was not fine - you ignored a major error that indicates instability in
your system.
with 3-4 steps of minimization also, but it didnt work (I have tried
with lincs warning off in NPT too). I have visualized the NVT output
trajectory and compared it with the initial structure too, and the
trajectory was fine.
You'll have to define what you think "fine" means, because if the simulation can
only run when disabling LINCS warnings, something has to be severely wrong.
I am unable to figure out the reason for why the system is blowing up. I
am following the drug-ligand simulation tutorial but still can't figure
out the problem. Can anyone suggest any possible means to overcome this
situation?
Yes, a general workflow is here:
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
The source of the error could be any number of things, including incorrect
topology, unsuitable .mdp settings, inappropriate system
construction/minimization, or any combination of those factors. Posting a
complete .mdp file would be helpful.
-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
