AMBER Archive (2009)

Subject: Re: [AMBER] reg-TMD

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Apr 29 2009 - 06:33:40 CDT

I can't really be any more help. you should look at your structure and see
why it might be stuck and unable to move closer to the reference.
also look in ene.f at the tgtmd() routine. the energy is 0.5 * tgtmdfrc *
nattgtrms * (rmsd - remd_ref)^2 or something like that.
i don't know how many atoms in your mask, but even with a large energy you
might need a higher tgtmdfrc. have you tried one? how did you decide on
0.016?

On Wed, Apr 29, 2009 at 7:25 AM, balaji nagarajan
<balaji_sethu_at_hotmail.com>wrote:

>
> 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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