[gmx-users] Potential Energy is positive on minimizing the system

[Anurag Dobhal]

Thanks a lot!




*Anurag Dobhal*
*Graduate Student (Bioprocess Technology)*
*Institute of Chemical Technology, Mumbai*
*Contact: +91 8898486877*


On Thu, Feb 23, 2017 at 9:10 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/23/17 9:07 AM, Anurag Dobhal wrote:
>
>> Dear Justin,
>>
>> I would like to know weather the parameters below are correct for NVT
>> equilibiration whicle doig a simulation in vaccum ?
>>
>> define = -DPOSRES ; position restrain the protein
>>
>
> If you don't have solvent, there's no reason to restrain anything.
> Normally one restrains the solute to allow the solvent to relax around it.
> Here, this serves no purpose.
>
> ; Run parameters
>> integrator = md ; leap-frog integrator
>> nsteps = 50000 ; 2 * 50000 = 100 ps
>> dt = 0.002 ; 2 fs
>> ; Output control
>> nstxout = 100 ; save coordinates every 0.2 ps
>> nstvout = 100 ; save velocities every 0.2 ps
>> nstenergy = 100 ; save energies every 0.2 ps
>> nstlog = 100 ; update log file every 0.2 ps
>> ; Bond parameters
>> continuation = no ; first dynamics run
>> constraint_algorithm = lincs ; holonomic constraints
>> constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
>> lincs_iter = 1 ; accuracy of LINCS
>> lincs_order = 4 ; also related to accuracy
>> ; Neighborsearching
>> ns_type = simple ; search neighboring grid cells
>>
>
> Note you also need cutoff-scheme = group here.
>
> nstlist = 0 ; 10 fs
>> rlist = 0.0 ; short-range neighborlist cutoff (in nm)
>> rcoulomb = 0.0 ; short-range electrostatic cutoff (in nm)
>> rvdw = 0.0 ; short-range van der Waals cutoff (in nm)
>> ; Electrostatics
>> coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
>>
>
> As I said before, you can't use PME (grompp will fail anyway, because you
> can't have PME without PBC).  Use a plain cutoff.
>
> pme_order = 0 ; cubic interpolation
>> fourierspacing = 0.0 ; grid spacing for FFT
>> ; Temperature coupling is on
>> tcoupl = V-rescale ; modified Berendsen thermostat
>> tc-grps = Other ; two coupling groups - more accurate
>> tau_t = 0.1 ; time constant, in ps
>> ref_t = 300 ; reference temperature, one for each group, in K
>> ; Pressure coupling is off
>> pcoupl = no ; no pressure coupling in NVT
>> ; Periodic boundary conditions
>> pbc = no ; 3-D PBC
>> ; Dispersion correction
>> DispCorr = EnerPres ; account for cut-off vdW scheme
>>
>
> Dispersion correction is also not applicable.
>
> -Justin
>
> ; Velocity generation
>> gen_vel = yes ; assign velocities from Maxwell distribution
>> gen_temp = 300 ; temperature for Maxwell distribution
>> gen_seed = -1 ; generate a random seed
>>
>> Thank You
>>
>>
>>
>>
>> *Anurag Dobhal*
>> *Graduate Student (Bioprocess Technology)*
>> *Institute of Chemical Technology, Mumbai*
>> *Contact: +91 8898486877*
>>
>>
>> On Thu, Feb 23, 2017 at 7:23 PM, Anurag Dobhal <
>> anurag.dobhal at nano-medicine.co.in> wrote:
>>
>> Thank you !
>>>
>>>
>>>
>>>
>>> *Anurag Dobhal*
>>> *Graduate Student (Bioprocess Technology)*
>>> *Institute of Chemical Technology, Mumbai*
>>> *Contact: +91 8898486877*
>>>
>>>
>>>
>>> On Thu, Feb 23, 2017 at 7:09 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>>
>>>> On 2/23/17 8:29 AM, Anurag Dobhal wrote:
>>>>
>>>> Thank you. Should I not use PME and PBC while performing simulations in
>>>>> Vaccum ?
>>>>>
>>>>>
>>>>> No, you should not.  Use no PBC and infinite cutoffs (all cutoffs set
>>>> to
>>>> zero) to mimic vacuum conditions.  Otherwise you're simulating some
>>>> type of
>>>> diffusely occupied crystal environment.
>>>>
>>>>
>>>> -Justin
>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>
>>>> Department of Pharmaceutical Sciences
>>>> School of Pharmacy
>>>> Health Sciences Facility II, Room 629
>>>> University of Maryland, Baltimore
>>>> 20 Penn St.
>>>> Baltimore, MD 21201
>>>>
>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>
>>>> ==================================================
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>>>>
>>>
>>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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> Gromacs Users mailing list
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