Thank you,
Sorry I have missed to put something else into in question
I mean I have created prmtop by using PBradii mbondi2 and then
parmed PRMT1_WT.prmtop
HMassRepartition
outparm PRMT1_WT_HP.prmtop
quit
So can I use this PRMT1_WT_HP.prmtop or I need to use PRMT1_WT.prmtop for dt=0.002
________________________________
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: Monday, November 28, 2016 6:22:13 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Etot = ************** with dtt=0.004
Time step is not related to pbradii.
You can set dt to any value, but above 0.002 is usually not ok without
something like mass repatriation.
On Nov 28, 2016 12:19 PM, "Thakur, Abhishek" <axt651.miami.edu> wrote:
> I have a small question Andrian that for dt=0.004 time step I need to add
> set default PBradii mbondi2 to make prmtop file.
>
> Can I use same parmtop file for dt=0.002 time step?
>
> Is it possible to run dt=0.003 time step?
>
> ________________________________
> From: Thakur, Abhishek
> Sent: Monday, November 28, 2016 6:06:21 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Etot = ************** with dtt=0.004
>
>
> Thank you.
>
> I have submitted the job with ncsm=100 and dt=0.002 and if I encounter
> some problem then I will take suggestion
>
> ________________________________
> From: Roitberg,Adrian E <roitberg.ufl.edu>
> Sent: Monday, November 28, 2016 5:47:43 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Etot = ************** with dtt=0.004
>
> Hi. Try the same input with dt=0.002 and tellbus what happens. Also do not
> use ncsm=1!!!!!
>
> Maybe 100, but not 1
>
> Adrian
>
>
>
> Sent from my Verizon, Samsung Galaxy smartphone
>
>
> -------- Original message --------
> From: "Thakur, Abhishek" <axt651.miami.edu>
> Date: 11/28/16 9:45 AM (GMT-07:00)
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Etot = ************** with dtt=0.004
>
> Yes I have used Hmassrepartitioning
>
>
> In other file I have found that it has given me that kindly check
> ()ncsm/=0) so I have tried my making ncsm=1 also but still same problem.
>
> I have also tried ntxo=2 but at some time step it gives me same error.
>
> Here in this I am expecting my dimer to open apart
>
> ________________________________
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Sent: Monday, November 28, 2016 5:39:05 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Etot = ************** with dtt=0.004
>
> that's a big time step. did you use H mas repartitioning?
>
>
> On Mon, Nov 28, 2016 at 11:29 AM, Thakur, Abhishek <axt651.miami.edu>
> wrote:
>
> > Hi everypne,
> >
> >
> > I am trying to run GB calculation with dtt=0.04,
> >
> > In the middle of the calculation I am finding something like this
> >
> >
> > NSTEP = 314000 TIME(PS) = 1306.000 TEMP(K) =********* PRESS =
> > 0.0
> > Etot = ************** EKtot = ************** EPtot =
> > **************
> > BOND = ************** ANGLE = 2805446.2151 DIHED =
> > 48742.6264
> > 1-4 NB = 0.0000 1-4 EEL = 0.0184 VDWAALS =
> > **************
> > EELEC = ************** EGB = -221738.0770 RESTRAINT =
> > 0.0000
> >
> >
> >
> > My script is
> >
> > &cntrl
> > imin=0,irest=1,ntx=5,
> > nstlim=2500000,dt=0.004,
> > ntf=2,ntc=2,ntb=0,ig=-1,
> > igb=5,cut=9999.0,rgbmax=25.0,
> > ntpr=500, ntwx=500, ntwr=10000,
> > saltcon=0.2, gamma_ln=50,
> > tempi=300.0, temp0=300.0,
> > ntt=3,tautp=1.0,
> > nscm=1,
> > &end
> > EOF
> >
> >
> >
> > Can anyone suggest me what is going wrong.
> > _______________________________________________
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> > AMBER.ambermd.org
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Received on Mon Nov 28 2016 - 10:00:03 PST
