Hi Thakur,
My guess is a problem with your initial structure. A classic example I have seen that works fine (or gives the illusion of working) at 2fs but fails at 4fs even with H Mass repartitioning is when you have ring penetration in your structure. E.g. a hydrogen atom on one residue is penetrating through a tryptophan ring for example. This will run with shake at 2fs and be stable, despite the fact that it is wrong from a physical perspective. However if one turns on H mass repartitioning and runs at 4fs then this eventually leads to either a shake failure or a blow up of the system. I'd go through and take a very careful look at your starting structure. Also if you can get a restart close to where it fails and then run with ntwx=1 you may be able to see from where the blow up happens and thus identify where the structural issue is.
Either way if you did the H mass repartioning correctly then it should run fine at 4fs with ntf=2,ntc=2 regardless of what solvents models you use etc. If it isn't working then I'd say it's almost certainly a structural or parameterization issue.
All the best
Ross
> On Nov 28, 2016, at 13:01, Nhai <nhai.qn.gmail.com> wrote:
>
>
>
>> 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.
>>>> _______________________________________________
>>>> AMBER mailing list
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Received on Mon Nov 28 2016 - 12:30:03 PST
