[gmx-users] Errors in Minimization using grompp
Justin A. Lemkul
jalemkul at vt.edu
Wed Jun 13 15:03:55 CEST 2012
On 6/13/12 8:59 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> Hi Justin,
> I managed it with your help that the minimization run worked. Now I
> prepared a .mdp file for the md run.
> Can you please tell me if the following .mdp file is correct?
>
> define = -DPOSRES
> integrator = md
> constraints = all-bonds
> emtol = 8
> niter = 15
The preceding two lines are irrelevant.
> nsteps = 50000
You haven't set a value for dt. The default is 0.001 ps, but with all bonds
constrained, you can set it to 0.002 for better performance.
> nstlist = 1
Neighbor searching at every step is extremely time-consuming, and largely
unnecessary. For EM, nstlist must be set to 1, but for MD, it should not. To
invoke the optimized all-vs-all kernels (in conjunction with the other settings
that trigger them), set nstlist=0 for a fixed neighbor list.
-Justin
> ns_type = simple
> rlist = 0
> comm-mode = angular
> comm-grps = System
> coulombtype = cut-off
> vdwtype = cut-off
> rcoulomb = 0
> rvdw = 0
> pbc = no
> epsilon_rf = 0
> implicit_solvent = GBSA
> gb_algorithm = HCT
> nstgbradii = 1
> rgbradii = 0
> gb_epsilon_solvent = 80
> gb_saltconc = 0
> sa_algorithm = Ace-approximation
> sa_surface_tension = -1
>
>
> Thank you,
> Eva
>
>
>>
>> On 6/13/12 7:55 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
>>> Hi!
>>> Thank you for your answer.
>>>
>>>> On 13/06/2012 6:44 PM, reisingere at rostlab.informatik.tu-muenchen.de
>>>> wrote:
>>>>> Hi everybody,
>>>>> I want to do a minimization of the hydrogens of my protein. Only the
>>>>> hydrogens.
>>>>
>>>> Doesn't really matter - nothing will move more than a fraction of an
>>>> Angstrom unless it's horribly wrong, in which case not moving the heavy
>>>> atoms won't help you.
>>>>
>>>>> And I want to do this with implicit solvent.
>>>>
>>>> Probably not worth the effort if you're just preparing for MD.
>>>
>>> Our goal is not an MD simulation of the protein. We plan a
>>> Poisson-Boltzmann electrostatics calculation. For that we need the heavy
>>> atoms as they are in the crystal structure (even 1 Angstroem movement
>>> would be too much) with good hydrogen atom position.
>>
>> With restraints on heavy atoms, your positions will not deviate very much
>> at
>> all. A 1 Angstrom movement would be huge in this case; I would expect
>> your
>> deviations to be orders of magnitude less.
>>
>>> We need to minimize, simulate, minimize, simulate the hydrogen atoms.
>>
>> I don't follow the logic here. You say you need to do an EM of the H
>> atoms in
>> order to do some PBSA calculation with no MD, but here you're doing two
>> iterations of EM and MD.
>>
>>> Implicit solvent is ok for us. (For a later MD run of the complete
>>> protein, we will use explicit solvent).
>>>
>>> This is the .mdp file:
>>>
>>
>> There are several problems here, most of which I've already stated, but
>> I'll
>> recapitulate them again.
>>
>>>
>>> define = -DPOSRES
>>> constraints = all-bonds
>>> integrator = steep
>>> nsteps = 30000
>>> vdwtype = cutoff
>>> coulombtype = cutoff
>>
>> As Mark said, these settings should be "cut-off" not "cutoff."
>>
>>> epsilon_rf = 0
>>> pbc = xyz
>>
>> For an implicit system, periodicity should be set to "no" and grompp will
>> warn
>> you about using angular COM removal (invoked below) if you leave it set as
>> is.
>>
>>> nstlist = 1
>>> ns_type = grid
>>> rlist = 1
>>> rcoulomb = 1.2
>>> rvdw = 1.2
>>
>> Finite cutoffs with implicit solvent will lead to instability and poor
>> energy
>> conservation. These three lines (rlist, rcoulomb, rvdw) should be set to
>> zero,
>> unless you're satisfied with artifacts.
>>
>>> rvdw_switch = 0.7
>>
>> This setting has no effect when using cutoffs.
>>
>>> comm-mode = angular
>>> comm-grps = System
>>> nstcgsteep = 1000
>>> emtol = 5.0
>>
>> Unless you've compiled with double precision, it is unlikely you will
>> achieve a
>> minimal force this low. The use of restraints is going to preclude most
>> movement in the system, so don't be surprised if grompp does not (and
>> cannot)
>> achieve this tolerance.
>>
>>> emstep = 0.01
>>> implicit_solvent = GBSA
>>> gb_algorithm = HCT
>>> nstgbradii = 1
>>> rgbradii = 1
>>
>> This should also be set to zero if the above neighbor searching parameters
>> are zero.
>>
>>> gb_epsilon_solvent = 80
>>> gb_saltconc = 0
>>> sa_algorithm = Ace-approximation
>>> sa_surface_tension = -1
>>>
>>> Additionally I have a question according to the vdwtype and coulombtype.
>>> Why do I have to set the two parameters to cutoff?
>>>
>>
>> Because settings like PME don't make sense for implicit solvent
>> calculations.
>> Plain cutoffs with finite values are almost never adequate for any
>> purpose, however.
>>
>> -Justin
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>>
>>
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>
>
>
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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