AMBER Archive (2009)

Subject: RE: [AMBER] reg-TMD

From: balaji nagarajan (balaji_sethu_at_hotmail.com)
Date: Wed Apr 29 2009 - 06:54:59 CDT

Dear Dr . Carlos Simmerling ,

I will look in files , i have not fixed the tgtmdfrc , i am doing trials ,

with this details i will check,

thanking you
regards
balaji

> From: carlos.simmerling_at_gmail.com
> Date: Wed, 29 Apr 2009 07:33:40 -0400
> Subject: Re: [AMBER] reg-TMD
> To: amber_at_ambermd.org
>
> 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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