I want to add that I am using a polarizable force field and POL3 water
model.
When I look at the output under Control Data for the Run, the only
difference I see is that in sander I also have this (I'm not sure if this
would mean anything) :
Polarizable options:
indmeth = 3, maxiter = 20, irstdip = 0, scaldip =
1
diptau = 11.00000, dipmass = 0.33000
Also I am using different versions of AMBER for both.
On Wed, Sep 13, 2017 at 12:25 PM, Chayya Bhargac <chayyachemistry.gmail.com>
wrote:
> I tried running this again (this time not in parallel).
>
> Interestingly, I got significantly different results for pmemd and sander.
> I run 10 steps of simulation and this is what I got (below). I checked
> that ..rst .in and .prmtop files are the same. The only difference was that
> I ran these in two different clusers (pmemd in TSCC and sander in Harvard
> Orchestra).
>
> Step 1 using sander:
>
> NSTEP = 1 TIME(PS) = 90.002 TEMP(K) = 299.13 PRESS =
> 0.0
>
> Etot = -238642.5964 EKtot = 73013.5247 EPtot =
> -311656.1211
>
> BOND = 418.8091 ANGLE = 1103.1341 DIHED =
> 1624.5376
>
> 1-4 NB = 536.1276 1-4 EEL = 8158.4711 VDWAALS =
> 17142.4812
>
> EELEC = -289239.4141 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> EPOLZ = -51400.2677
>
> Dipole convergence: rms = 0.364E-04 temperature = 0.00
>
> ------------------------------------------------------------------
>
>
>
> Step 1 using pmemd:
>
>
>
> NSTEP = 1 TIME(PS) = 90.002 TEMP(K) = 299.04 PRESS =
> 0.0
>
> Etot = -186990.7423 EKtot = 72992.1028 EPtot =
> -259982.8451
>
> BOND = 418.8091 ANGLE = 1103.1341 DIHED =
> 1624.5376
>
> 1-4 NB = 536.1276 1-4 EEL = 8158.4711 VDWAALS =
> 17142.4812
>
> EELEC = -288966.4058 EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> Ewald error estimate: 0.4460E-06
>
> ------------------------------------------------------------------
>
> On Tue, Sep 12, 2017 at 7:25 AM, David A Case <david.case.rutgers.edu>
> wrote:
>
>> On Mon, Sep 11, 2017, Chayya Bhargac wrote:
>> >
>> >
>> > I am trying to run a NVT simulation on AMBER.
>> > When I try running the simulation with sander,
>> > it doesn't run and I get an error (shown below).
>> >
>> > But when, I run the same using pmemd, it runs to
>> > completion. What could be the reason for this?
>>
>> Odd. Are these parallel runs?
>>
>> I'll repeat the usual debugging strategy: the sander run fails on steps 4
>> and
>> 5. So, you need to run a short simulation (say nstlim=100), and set
>> ntpr=1,
>> in order to get any information on what is going on. Do the same thing
>> for
>> pmemd. See if the intial step is the same; see when the two runs diverge
>> from each other.
>>
>> ....dac
>>
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Wed Sep 13 2017 - 10:00:02 PDT
