AMBER Archive (2009)

Subject: RE: [AMBER] reg-TMD

From: balaji nagarajan (balaji_sethu_at_hotmail.com)
Date: Wed Apr 29 2009 - 06:25:50 CDT

Thank you

Dr . Carlos Simmerling

The structures which i took having an all atom RMSD 15.785,
and I am doing it in 300K , here I have given the out put of my run .

I have not got a clear idea still , if you can look in to the out put file and tell me where the problem is

then it will be helpfull to me
-------------------------------------------------------------

 NSTEP = 209600 TIME(PS) = 329.600 TEMP(K) = 301.34 PRESS = 85.2
 Etot = -44293.7387 EKtot = 8602.5880 EPtot = -52896.3267
 BOND = 340.1219 ANGLE = 652.3955 DIHED = 870.2178
 1-4 NB = 333.5833 1-4 EEL = -6219.4487 VDWAALS = 5327.8308
 EELEC = -54699.0128 EHBOND = 0.0000 RESTRAINT = 497.9856
 EAMBER (non-restraint) = -53394.3123
 EKCMT = 3781.3521 VIRIAL = 3526.3339 VOLUME = 138664.3560
                                                    Density = 1.0642
 Ewald error estimate: 0.2079E-05
Current RMSD from reference: 6.930
Current target RMSD: 0.000
 ------------------------------------------------------------------------------

 NSTEP = 209650 TIME(PS) = 329.650 TEMP(K) = 302.16 PRESS = 219.8
 Etot = -44278.5776 EKtot = 8626.1189 EPtot = -52904.6965
 BOND = 324.7662 ANGLE = 659.2596 DIHED = 856.1542
 1-4 NB = 348.0356 1-4 EEL = -6250.4139 VDWAALS = 5445.2923
 EELEC = -54785.0230 EHBOND = 0.0000 RESTRAINT = 497.2324
 EAMBER (non-restraint) = -53401.9289
 EKCMT = 3787.8113 VIRIAL = 3129.5104 VOLUME = 138718.1890
                                                    Density = 1.0638
 Ewald error estimate: 0.9312E-05
Current RMSD from reference: 6.925
Current target RMSD: 0.000
-------------------------------------------------

thanking you
balaji
UOM

> From: carlos.simmerling_at_gmail.com
> Date: Wed, 29 Apr 2009 06:28:35 -0400
> Subject: Re: [AMBER] reg-TMD
> To: amber_at_ambermd.org
>
> it's good to always read the output file carefully. in your case I think it
> probably never says anything about reading your weight change, since you
> don't have nmropt=1. also you are right that a force constant of 0.016 is
> too small- look at your restraint energy in the output file, it will be
> small. it helps to have an idea of what is a "large" energy. in this case I
> don't know your initial rmsd, but you can use that difference and the fact
> that it is a harmonic restraint to estimate when the restraint energy will
> be. you want it to be well above the thermal energy of about 0.5 kcal. it
> may take a bit of trial and error because it depends on how easy it is to
> get your system to change rmsd- but start at tgtmdfrc=1 and go from there.
>
> On Wed, Apr 29, 2009 at 12:16 AM, balaji nagarajan <balaji_sethu_at_hotmail.com
> > wrote:
>
> >
> > 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
> > > >
> > > >
> > > >
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