On 9/1/15 9:40 AM, Nima Soltani wrote:
Hi everyone
I am simulating the interactions between a small peptide and different
metallic surfaces solvated in TIP3P water.
So far i have simulated 3 different surfaces correctly , however the last
surface becames unstable after nearly 2 ns of simulation.
I did an EM step again and reduced time step to half (i.e. 0.5 fs) however
it didn't work ... I've even set lincs-warnangle to its maximum value(=
90), howeer it failed again . I don't have any idea how to fix it
The surface is Polarizable by using *Drude* oscillators and i think these
oscillatoras are the cause of problems .
Step Time Lambda
2270000 2270.00000 0.00000
Energies (kJ/mol)
U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14
3.87510e+02 6.15054e+01 1.98057e+01 -5.57740e+01 6.96654e+01
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
2.93372e+03 8.97847e+04 -6.19085e+03 -7.47168e+05 2.44969e+03
COM Pull En. Potential Kinetic En. Total Energy Temperature
1.39457e-03 -6.57708e+05 1.23026e+05 -5.34682e+05 3.09198e+02
Pres. DC (bar) Pressure (bar) Constr. rmsd
-2.03445e+02 -9.16454e+01 1.80260e-06
-------------------------------------------------------
Program gmx, VERSION 5.0.5
Source code file:
/share/apps/gromacs-5.0.5/gromacs-5.0.5/src/gromacs/mdlib/constr.c, line:
224
Fatal error:
Too many LINCS warnings (1000)
If you know what you are doing you can adjust the lincs warning threshold
in your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Thanks in advance for any suggestions / assistance
You'll have to describe in exact detail what you're doing. It's very easy to
break a polarizable model. What are the sources of the parameters? Have these
parameters been validated in the context of TIP3P? This sounds like a very
weird combination to me, to have part of the system polarizable and the rest not.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
[email protected] | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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