normal LINCS and pressure coupling

  • satyan
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10 years 3 months ago #379 by satyan
LINCS and pressure coupling was created by satyan
Hi all,
I am facing problems related to LINCS and pressure coupling. Either the simulations list 1 to 4 pairs of atoms involved in the LINCS warning and the pressure sclaing warnings follow OR, just the pressure warnings appear (without LINCS warning). I changed lincswarnangle from 30 to 90 and also tried different values of tau_p(1.0, 3.0, 5.0) and compressibility (3e-4, 3e-5, 5e-5). Although the FAQ section recommends tau_p of 1-5 and compressibilty e-4 to e-3. But i do see publications using values of 5e-6 and 5e-5. I would liek to know, how should one select these values, or are these based on just trial and error. I know that these LINCS warnings are related to unquilibriated structures. I am simulating a structure form NMR. Two different models were tried form NMR ensemble. In one case I even did 5ns atomistic MD to relax, and used as input for converting to CG model. The CG struture was also relaxed slowly. The strange thing is that the LINCS warning appear after 50-80ns (time-step of 20fs). I also tried rlist of 1.4. I am runing out of diagnosis and would like to ask you all.

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10 years 2 months ago #381 by xavier
Replied by xavier on topic LINCS and pressure coupling
the tau_P/T and compressibility should not be modified from the original mdp file you can get from the Download section.

This said the lincs warning you seem to experience should not be there. You have to check your topology and identify which residue(s) is responsible for these warning.

My experience is that when lincs warning appear consistently it is often that the topology is not correct. There are many things that can go wrong. Check your atomistic pdb file and the gro and the topology.


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