> On Nov 28, 2016, at 12:45 PM, Thakur, Abhishek <axt651.miami.edu> wrote:
>
>
> 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
>
>
You can use either of them for 2fs run.
But for debugging, you should use your original prmtop
Hai
>
> ________________________________
> 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 mailing list
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Received on Mon Nov 28 2016 - 10:30:02 PST
