Re: Re: restraining the protein not to move during equilibration

From: Lewyn Li (lewynli_at_gmail.com)
Date: Mon Oct 09 2006 - 10:52:55 CDT

Hi Dhiraj,

        Both "consref" and "conskfile" are explained in the NAMD manual:

http://www.ks.uiuc.edu/Research/namd/2.6/ug/node28.html

        The "conskfile" contains the harmonic spring constants in the X
column of the file "protein_cons.pdb" in your case. For the value of
k, usually I reduce the restraint from 5 to 3 to 1 in three
sequential steps of restrained equilibration. This is what Anya, Tim
and I were discussing in the thread I sent you. The e-mail by Tim
contains a lot of useful tips on how to minimize and equilibrate in
general.

        By the way, why not put the spring constants in either the O- or the
B-column? Putting them in the X column means you would have to
replace the x-coordinates of the pdb with a bunch of spring
constants, which is a bit of work that may not be necessary.

        Hope this helps!

LEWYN

On Oct 9, 2006, at 10:23 AM, Dhiraj Srivastava wrote:

> Hi Lewyn
> thanks for help. but how sholuld i make my file for
> constraining protein. i have written my way of doing this in the
> previous mail and i am again writing it.
>
> Hi All
> I want to keep the position of my protein atom fixed while
> equilibrating the system. for that i am planning to use following
> script.
>
> #constraints
> constraints on
> consref protein_only.coor
> conskfile protein_cons.pdb
> conskcol X
> how should i make the "consref" and "conskfile". i am thinking of
> setting the occupancy of protein atoms 1 for "conskfile". is it
> correct? then what should be the "consref" file.
>
>
>
>
> On 10/9/06, Lewyn Li <lewynli_at_gmail.com> wrote:
> Dhiraj,
>
>
> Several of us were involved in a discussion on this topic a little
> while ago. Here is the thread:
>
>
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/4357.html
>
>
> Hope this helps!
>
>
>
>
> LEWYN
>
> On Oct 9, 2006, at 12:36 AM, Dhiraj Srivastava wrote:
>
>> also i am planning my simulation as first minimizing and
>> equilibrating the system with constraint on and then constraint
>> off. is this the correct sequence or should i first minimize and
>> equilibrate the system with constraint off, then constraint on and
>> then again constraint off.
>>
>> On 10/8/06, Dhiraj Srivastava <dhirajks_at_gmail.com > wrote:
>> Hi All
>> I want to keep the position of my protein atom fixed while
>> equilibrating the system. for that i am planning to use following
>> script.
>>
>> #constraints
>> constraints on
>> consref protein_only.coor
>> conskfile protein_cons.pdb
>> conskcol X
>> how should i make the "consref" and "conskfile". i am thinking of
>> setting the occupancy of protein atoms 1 for "conskfile". is it
>> correct? then what should be the "consref" file.
>>
>>
>> --
>> Dhiraj Kumar Srivastava
>> Department of Chemistry
>> University of Missouri-Columbia
>> MO, 65211
>>
>>
>>
>>
>> --
>> Dhiraj Kumar Srivastava
>> Department of Chemistry
>> University of Missouri-Columbia
>> MO, 65211
>> Ph. no. 001-573-639-0153
>
>
>
>
>
> --
> Dhiraj Kumar Srivastava
> Department of Chemistry
> University of Missouri-Columbia
> MO, 65211
> Ph. no. 001-573-639-0153

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