Re: Simulation of the membrane protein

From: James Starlight (jmsstarlight_at_gmail.com)
Date: Thu Sep 05 2013 - 00:35:26 CDT

Aron, thanks for suggestions!

I've done all such operations but the results the same.

If it possible I can share pdb as well as psf files of my complex produced
after ionization by VMD.

Perhaps some problems might be also due to the insertion (automate
generation of the complex psf which have been done according to the script
provided in the
http://users.mccammon.ucsd.edu/~rlaw/ctbp_workshop_rlaw.htm) If
someone have modified version of such script for quick insertion and
deletion of the lipids in the aligned bi-layer I'll be thankful for it as
well as for example conf file for production run of the protein-lipid
system made with ch27 params

Thanks again,

James

2013/9/4 Aron Broom <broomsday_at_gmail.com>

> just on the PBC thing, although I somewhat doubt it's the answer. Your
> cellBasisVector values don't agree with what you posted from VMD. For
> instance, you have cellBasisVector3 as 98.2, but that value from VMD should
> be (93.664 - 0.594) which is 93.07, the others are off by much less.
>
> Some other things to try before the restraints:
>
> - increase minimization steps (go 10x what it currently is maybe)
> - decrease timestep (go to 0.5 for instance)
> - decrease temperature (start at something quite low like < 100K)
>
> Also, you said analysis doesn't reveal artifacts, but if there is a
> constraint failure, then something went flying off at high speed. So you
> might want to decrease you DCDFrequency or whatever the variable is called
> so you can see what is leading to the problem, particularly if this is
> happening early on.
>
> ~Aron
>
>
> On Wed, Sep 4, 2013 at 12:16 PM, James Starlight <jmsstarlight_at_gmail.com>wrote:
>
>> 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
>>
>>
>>
>>
>>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
>

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