Simulation of the membrane protein

From: James Starlight (jmsstarlight_at_gmail.com)
Date: Wed Sep 04 2013 - 11:16:35 CDT

Dear NAMD Users!

Recently I've forced with the problem of simulation membrane protein system.

I've done all steps according to the official tutorial

1) building POPE membrane using VMD

2) generated PSF files of my protein

2) inserted protein into membrane and removed overlapped lipids

3)solvated and ionized my system using VMD

Than I've minimized my system and tried pack lipids but simulation have
been crashed

on this step I've froze all water ion and protein atoms and run short
simulation in NPT according to the tutorial parameters.

as the result I've obtained

Info: ABSOLUTE IMPRECISION IN FAST TABLE ENERGY: 1.69407e-21 AT 11.9974
Info: RELATIVE IMPRECISION IN FAST TABLE ENERGY: 1.13046e-16 AT 11.9974
Info: INCONSISTENCY IN FAST TABLE ENERGY VS FORCE: 0.000290274 AT 0.251946
Info: INCONSISTENCY IN VDWA TABLE ENERGY VS FORCE: 0.0040507 AT 0.251946
Info: INCONSISTENCY IN VDWB TABLE ENERGY VS FORCE: 0.00150189 AT 0.251946
Pe 2 hosts 15 local and 15 remote patches for pe 2
Pe 3 hosts 15 local and 15 remote patches for pe 2
Pe 1 hosts 10 local and 10 remote patches for pe 2
Pe 0 hosts 23 local and 22 remote patches for pe 2
Info: useSync: 1 useProxySync: 0
Info: Startup phase 10 took 0.037595 s, 102.809 MB of memory in use
Info: Startup phase 11 took 0.000133991 s, 102.973 MB of memory in use
Info: Startup phase 12 took 0.000496864 s, 103.18 MB of memory in use
Info: Finished startup at 1.20948 s, 103.34 MB of memory in use

TCL: Running for 250000 steps
Pe 2 has 63 local and 62 remote patches and 1701 local and 1674 remote
computes.
ERROR: Constraint failure in RATTLE algorithm for atom 35875!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely; see error messages above.
====================================================

its remarkable that such error have occurred even with applied position
restraints to ALL atoms of my system. In addition I've tried to make such
packing for pure hydrated lipids but forced with the same error too.

 Might it be due to some problems with the PBC definition (I've done
manually definition of the xyz dimensions using vmd as you can see below

atomselect0
>Main< (GPRC_namd) 2 % measure minmax $everyone
{1.0085545778274536 0.6706096529960632 0.593999981880188}
{104.46700286865234 102.0479965209961 93.66400146484375}

measure center $everyone
52.83515548706055 51.502288818359375 46.488792419433594

and than defined that in the conf file:

cellBasisVector1 103.1 0 0
cellBasisVector2 0 100.9 0
cellBasisVector3 0 0 98.2
cellOrigin 52.80777359008789 51.45378112792969 46.48970031738281

during analysis of the minimization I've not observed any artifacts.

What also membrane simulation options should I take into account?

Thanks for help,

James

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