[gmx-users] Correct .mdp file for Amber99SB-ILDN ff implementation in Gromacs
Mohsen Ramezanpour
ramezanpour.mohsen at gmail.com
Thu Jul 14 18:40:55 CEST 2016
Thanks Joao and Justin for your comments,
As Justin mentioned, I followed the original articles on this force field.
However, I was not sure if the same parameters can be transferred to
Gromacs or not.
The only thing different was the initial temperature of 50K and increasing
it to 310 K through simulation. I agree with you on this. But I had the
following reason in mind. Please correct me if I am wrong.
Since 310 is a normal T, 50 should change to 310, not a big difference.
But, what do you think if you want to have 400 or 450 K as the equilibrium
T? In this case, is not it better to just start with a smaller number, say
300 K, and raise it to 450 K? This is just an example to justify what I
meant.
Cheers
Mohsen
On Thu, Jul 14, 2016 at 4:23 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 7/14/16 4:37 AM, João Henriques wrote:
>
>> I was wondering if I should modify any terms because of using Gromacs
>>>
>> package?
>>
>> It's good practice to set your key parameters as close as possible to
>> theirs. I am not familiar with Desmond, but I assume many of its
>> parameters
>> have similar counterparts in Gromacs. If you plan on (significantly)
>> modifying any parameters, you necessarily need to perform a sanity check
>> and validate your results.
>>
>> To me, and this is my personal opinion, there are some parameters in your
>> email that seem a bit strange. Why 1 femtosecond integration time for the
>> equilibration? 2 fs with LINCS should work fine. Why do you set two
>> different Fourier spacings? Plus, why set the last one (the one that is
>>
>
> The OP will undoubtedly get a fatal error from repeating fourierspacing.
> This comes from too literally following the paper's methods. The authors
> in that case specified 32 grid points in each spatial dimension, but this
> is a system-dependent quantity, and for a large system this may be too
> inaccurate. The OP should probably leave the default fourierspacing (0.12)
> alone and not set fourier-n[xyz] explicitly.
>
> effectively used) to zero? Where did you get that 1.05 for the rlist? Is
>> that 0.05 going to make any difference? Also, double check the pressure
>> and
>>
>
> This is following the paper, in which they state it explicitly as rlist.
> I agree that such a short distance is unlikely to have a practical effect,
> but in the effort to follow the force field's validated run parameters, it
> is correct.
>
> In GROMACS, using the Verlet cutoff scheme with rlist = rcoulomb = rvdw =
> 1.0 would be a faithful representation of what the AMBER99SB-ILDN paper did.
>
> temperature coupling constants. Finally, why are you generating an initial
>> temperature of 50K and then have it coupled to 310 K?
>>
>> These are just a few issues that come to mind after a quick read of your
>> email. There may be others, and I may also be wrong in my assessment... I
>> personally believe that there is no single recipe to performing
>> simulations, and I find that it is always better to modify only what you
>> need and understand, instead of following someone's work blindly. After
>> all, you need you understand what and why you do it and, unless you're
>> trying to replicate their work, no single set of parameters should be
>> absolutely "right". You need, of course, to be sensible when changing them
>> and check/validate your results afterwards.
>>
>>
> Agreed, except in the case of cutoffs and water models. These are as much
> a part of the force field as the parameters themselves. The effects due to
> mistakes can be subtle and unpredictable, so unless the user is prepared to
> do a careful, systematic study of cutoff effects (which is probably a paper
> or two in and of itself), then that user should follow the people who
> actually made the force field. A model is only valid under the conditions
> which are known to be valid :)
>
> -Justin
>
>
> Hope it helps,
>> Best regards,
>> João
>>
>> On Wed, Jul 13, 2016 at 11:34 PM, Mohsen Ramezanpour <
>> ramezanpour.mohsen at gmail.com> wrote:
>>
>> Dear Gromacs-users,
>>>
>>> I am interested in simulation of protein-ligand system.
>>>
>>> To do so, I have chosen the amber99sb-ildn force field.
>>>
>>> Reading through the original paper on this force filed by D.E.Shaw group
>>> (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2970904/) I have made the
>>> following equilibriu,.mdp and production-run.mdp files. I am not sure of
>>> it, though. Please correct me if I am wrong.
>>>
>>> The authors have used Desmond package not Gromacs for their simulations.
>>> I was wondering if I should modify any terms because of using Gromacs
>>> package?
>>> (This is the case for using charmm force field in Gromacs).
>>>
>>> I read other posts in gromacs list but I could not get any clear answer
>>> for
>>> this.
>>>
>>> Thanks in advance for your comments
>>> Cheers
>>> Mohsen
>>>
>>>
>>> for Equilibrium.mdp, I made:
>>>
>>> define =
>>>
>>> ; RUN CONTROL PARAMETERS
>>> integrator = md ;
>>> tinit = 0 ;
>>> dt = 0.001 ; 1 femtosecond time step for
>>> integration
>>> nsteps = 500000 ; 1 ns
>>>
>>> ; OUTPUT CONTROL OPTIONS
>>> nstxout = 0 ; Writing full precision
>>> coordinates
>>> nstvout = 0 ; Writing velocities
>>> nstfout = 0 ; writing forces
>>> nstlog = 2500 ; Writing to the log file
>>> nstenergy = 2500 ; Writing out energy information
>>> nstxtcout = 2500 ; Writing coordinates every 5 ps
>>> energygrps = Protein ligand Water_and_ions
>>> xtc_precision = 1000
>>> xtc-grps = System
>>>
>>> ; NEIGHBORSEARCHING PARAMETERS
>>> nstlist = 10
>>> ns-type = Grid
>>> pbc = xyz
>>> rlist = 1.05
>>> cutoff-scheme = Verlet
>>> nstcalclr = 1
>>>
>>> ; OPTIONS FOR ELECTROSTATICS AND VDW
>>> coulombtype = PME
>>> rcoulomb = 1.0
>>> fourierspacing = 0.1
>>> vdw-type = cut-off
>>> rvdw = 1.0
>>> optimize_fft = yes
>>> fourierspacing = 0
>>> fourier-nx = 32
>>> fourier-ny = 32
>>> fourier-nz = 32
>>> pme-order = 4
>>>
>>> ; Temperature coupling
>>> Tcoupl = v-rescale ; in the original paper
>>> it
>>> is Nose-Hoover thermostat
>>> tc-grps = Protein_ligand Water_and_ions
>>> tau_t = 1.0 1.0
>>> ref_t = 310 310
>>>
>>> ; Pressure coupling
>>> Pcoupl = nose-hoover
>>> Pcoupltype = isotropic
>>> tau_p = 5.5
>>> compressibility = 4.5e-5
>>> ref_p = 1.00
>>> refcoord_scaling = com
>>>
>>> ; GENERATE VELOCITIES FOR STARTUP RUN
>>> gen_vel = yes ; Assign velocities to particles by
>>> taking them randomly from a Maxwell distribution
>>> gen_temp = 50.0 ; Temperature to generate corresponding
>>> Maxwell distribution
>>> gen_seed = 1235 ; Seed for (semi) random number
>>> generation.
>>>
>>> ; OPTIONS FOR BONDS
>>> constraint-algorithm = SHAKE
>>> constraints = h-bonds
>>>
>>>
>>> and for production-run.mdp, I just change the
>>>
>>> dt = 0.002 ; 1 femtosecond time step
>>> for
>>> integration
>>> constraint-algorithm = LINCS
>>> constraints = all-bonds
>>> gen_vel = no
>>>
>>>
>>>
>>>
>>>
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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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