AMBER Archive (2009)

Subject: RE: [AMBER] reg-TMD

From: balaji nagarajan (balaji_sethu_at_hotmail.com)
Date: Wed Apr 29 2009 - 20:44:32 CDT

Dear Shaowen ,

thank you
i will try it out .,

regards
balaji
UOM

> From: shaowen.hu-1_at_nasa.gov
> To: amber_at_ambermd.org
> Date: Wed, 29 Apr 2009 15:56:07 -0500
> Subject: RE: [AMBER] reg-TMD
>
> You may try adding nmropt=1 in your script, and change tgtrmsd to 16.0. I encountered a same problem before.
>
> Best,
> Shaowen
>
> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On Behalf Of balaji nagarajan
> Sent: Tuesday, April 28, 2009 11:16 PM
> To: amber forumnew
> Subject: RE: [AMBER] reg-TMD
>
>
> Dear Dr . Carlos Simmerling ,
>
> I am sorry i may not be clear , to explain,
>
> I am giving my script below ,
> if not the force has to be changed , then what shall i have to do ,
> i am not able to get your words , i am sorry .
> ------------------------------------------------------------------
> &cntrl
> imin = 0, ntx=1, nstlim=3000000,
> irest =0,
> ntb = 2,
> pres0 = 1.0,
> ntp =1 ,
> ntxo = 1,
> ntx =1,
> tempi =300.0,
> ntc=2,
> ntf = 2,
> nscm = 0,
> ntwr = 50
> ntpr = 50,
> ntwx = 50,
> ntwv =50,
> ntwe = 50,
> ntt = 3,
> gamma_ln = 1.0,
> temp0 = 300.0,
> dt = 0.001,
> scee=1.2,
> cut =8.0,
> itgtmd=1,
> tgtrmsd =0.0 ,
> tgtmdfrc =0.016,
> tgtfitmask= ":1- 76"
> tgtrmsmask= ":1- 76"
> /
>
>
>
> &wt
> TYPE='TGTRMSD', istep1=1, istep2=3000000,
> value1 =16.0, value2 = 1.0,
> / &wt
> type="END"
> -------------------------------------------------------
> The current Rmsd value stays at 7.1 itself and its not going down towards 0
>
> regards
> balaji
> UOM
>
>
> > From: carlos.simmerling_at_gmail.com
> > Date: Tue, 28 Apr 2009 13:48:18 -0400
> > Subject: Re: [AMBER] reg-TMD
> > To: amber_at_ambermd.org
> >
> > using the force to control the transition rate is probably not useful,
> > change the target value instead. it looks like this is what you are doing,
> > so I am not sure what you mean by it not working. is the rmsd value not what
> > you requested?
> >
> >
> > On Tue, Apr 28, 2009 at 11:23 AM, balaji nagarajan <balaji_sethu_at_hotmail.com
> > > wrote:
> >
> > >
> > > Dear Amber ,
> > >
> > > Thank you
> > > Dr. Ccarlos Simmerling
> > > and Shaowen
> > >
> > > I have solved my problem , now the Tmd in explicit water in going
> > > good ,
> > >
> > > the problem is with the parameter file , it has been corrected
> > >
> > > i need another clariffication regarding the
> > > weighting option
> > >
> > > I gave a force and after some time the rmsd is not changing its going at a
> > > constant value
> > > if i give the greater force i can not view the transition clearly because
> > > it moves from one structure to the other in
> > > a rapid manner ,
> > >
> > > is there any option to change the weight after some time during the run
> > > like changing both force and the weighting option ,
> > > /
> > > &wt
> > > TYPE='TGTRMSD', istep1=1, istep2=1000000,
> > > value1 = 16.00, value2 = 8.00,
> > >
> > > /
> > > &wt
> > > TYPE='TGTRMSD', istep1=1000000, istep2=2000000,
> > > value1 = 8.00, value2 =1.00,
> > >
> > >
> > > /
> > >
> > > or is there any way to fix this problem .,
> > >
> > >
> > > balaji
> > > UOM
> > >
> > >
> > >
> > > _________________________________________________________________
> > > How fun is this? IMing with Windows Live Messenger just got better.
> > >
> > > http://www.microsoft.com/india/windows/windowslive/messenger.aspx_______________________________________________
> > > AMBER mailing list
> > > AMBER_at_ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _________________________________________________________________
> Twice the fun-Share photos while you chat with Windows Live Messenger.
> http://www.microsoft.com/india/windows/windowslive/messenger.aspx_______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

_________________________________________________________________
Twice the fun—Share photos while you chat with Windows Live Messenger.
http://www.microsoft.com/india/windows/windowslive/messenger.aspx_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber