Re: Umbrella sampling using dihedral angle

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Jan 24 2012 - 11:21:34 CST

wrapAround is a keyword to be defined inside dihedral. Check here for
future reference:
http://www.ks.uiuc.edu/Research/namd/2.8/ug/node55.html#SECTION000132200000000000000

On Tue, Jan 24, 2012 at 12:19 PM, Buddhadev Maiti <bmaiti_at_gsu.edu> wrote:

> Dear Giacomo,
>
> Thank you very much for your great help. Exactly I am asking this
> question. But I am facing problem where do I need to put wrapAround 180.
> If I put covarsconfig or namd config file, both cases I am facing problem,
> it gives me error that:
> colvars: Error: keyword "wraparound" is not supported, or not recognized
> in this context.
> ERROR: wrapAround
>
> Could you please help me, it will great help for me.
> Have a nice day,
> Thanks again,
> Maiti
> ------------------------------
> *From:* Giacomo Fiorin [giacomo.fiorin_at_gmail.com]
> *Sent:* Tuesday, January 24, 2012 10:38 AM
> *To:* Buddhadev Maiti
> *Cc:* namd-l_at_ks.uiuc.edu
> *Subject:* Re: Umbrella sampling using dihedral angle
>
> Hello Maiti, if you only want positive values of the dihedral for output
> purposes, you can use wrapAround 180. Is that what you need?
>
> On Sun, Jan 22, 2012 at 11:17 PM, Buddhadev Maiti <bmaiti_at_gsu.edu> wrote:
>
>> Dear Giacomo,
>>
>> Thank you very much for your all kind of great help. Finally I decided to
>> do umbrella sampling using dihedral angle. I have another question. I would
>> like to print positive value of dihedral angle in us1.colvars.traj, could
>> you please reply me what kind of option do I need to put in namd
>> configuration file.
>>
>>
>> Have a nice day,
>>
>> Thanks,
>>
>> Maiti
>>
>>
>> covarsconfig:
>>
>>
>> Colvarstrajfrequency 100
>>
>> Colvarsrestartfrequency 100
>>
>> colvar {
>>
>> name us
>>
>> dihedral {
>>
>> group1 {
>>
>> atomnumbers { 3639 3640 3642 3644 3645 3646 3648 3649 }
>>
>> }
>>
>> group2 {
>>
>> atomnumbers { 3634 3636 3637 3650 3652 3655 3656 3657 3658 3659 }
>>
>> }
>>
>> group3 {
>>
>> atomnumbers { 3663 3665 3666 3682 3684 3687 3688 3689 3690 3691 }
>>
>> }
>>
>> group4 {
>>
>> atomnumbers { 3668 3669 3671 3672 3673 3674 3678 3677 3680 3681 }
>>
>> }
>>
>> }
>>
>> }
>>
>> harmonic {
>>
>> colvars us
>>
>> centers -1.70350780500746e+02
>>
>> forceConstant 10.0
>>
>> }
>>
>>
>> us1.colvars.traj:
>>
>> # step us
>>
>> 0 -1.78341424821100e+02
>>
>> 100 -1.78341417695444e+02
>>
>> 200 -1.78341427134217e+02
>>
>> 300 -1.78341453149846e+02
>>
>>
>> But I like to print this way:
>>
>> # step us
>>
>> 0 1.78341424821100e+02
>>
>> 100 1.78341417695444e+02
>>
>> 200 1.78341427134217e+02
>>
>> 300 1.78341453149846e+02
>>
>
>

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