[gmx-users] Semiisotropic pressure coupling

[shivangi nangia]

>
> Dear Justin,
>

Thanks for the reply.

The link you have mentioned says the parameters are for GROMACS 5.0

I am using an older version, 4.6.1

Is there another link/suggestions for that version.

Sorry, I forgot to mention.

On trying to use those parameters with my version of GROMACS, I get the
error:

ERROR 1 [file md.mdp, line 78]:
  Invalid enum 'force-switch' for variable vdw-modifier, using
  'Potential-shift-Verlet'
  Next time use one of: 'Potential-shift-Verlet' 'Potential-shift' 'None'
  'Potential-switch' 'Exact-cutoff'


The mdp options manual says:

*Force-switch*Smoothly switches the forces to zero between *rvdw-switch*
 and *rvdw*. This shifts the potential shift over the whole range and
switches it to zero at the cut-off. Note that this is more expensive to
calculate than a plain cut-off and it is not required for energy
conservation, since *Potential-shift* conserves energy just as well

Can I use Potential-shift instead of my version?
Kindly suggesr.
Thanks in advance.



On Thu, Feb 12, 2015 at 10:30 PM, shivangi nangia <shivangi.nangia at gmail.com
> wrote:

>
>
> Dear Justin,
>>
>
> Thanks for the reply.
>
> The link you have mentioned says the parameters are for GROMACS 5.0
>
> I am using an older version, 4.6.1
>
> Is there another link/suggestions for that version.
>
> Thanks so much,
>
> Best,
> sxn
>
>>
>>
>> On 2/12/15 8:15 PM, shivangi nangia wrote:
>>
>>> Hello All,
>>>
>>> I am doing all-atom simulation with charmm 36 ff (obtained from reverse
>>> CG
>>> using the script provided by Tsjerk)
>>> The system consists of popc, 21 AA protein, water and ions.
>>>
>>> After reverse CG I did short EM and 5 ns NVT simulation.
>>> However, when I do NPT simulation, the area per lipid drops from 67 ang2
>>> to
>>> 57 within 1 ns ( x and y dimensions decrese and z increases).
>>>
>>> I am using semiisotropic pressure coupling.
>>>
>>> I have a question regarding that.
>>> I noticed in example .mdps and the tutorial by Justin Lemkul
>>>
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>>> gmx-tutorials/membrane_protein/Files/npt.mdp
>>>
>>>
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>>> gmx-tutorials/membrane_protein/Files/md.mdp
>>>
>>>
>>> tau_p is specified, the ref_p and compresibility is same, does not that
>>> mean essentially I am doing isotropic coupling?
>>>
>>>
>> No, that does not indicate isotropic pressure coupling.  The full
>> pressure tensor is used to calculate pressures in the x-y and z dimensions
>> separately. The values of tau_p and compressibility are simply used for
>> calculating the response time of the barostat.
>>
>> The problem is that your nonbonded settings are incorrect:
>>
>>  ; nblist cut-off
>>> rlist                    = 1.2
>>>
>>> ; OPTIONS FOR ELECTROSTATICS AND VDW
>>> ; Method for doing electrostatics
>>> coulombtype              = PME
>>> rcoulomb-switch          = 0
>>> rcoulomb                 = 1.2
>>> fourierspacing           = 0.16
>>> pme_order                = 4
>>> optimize-fft            = yes
>>> ; Method for doing Van der Waals
>>> vdw-type                 = switch
>>> ; cut-off lengths
>>> rvdw-switch              = 1.0
>>> rvdw                     = 1.2
>>>
>>>
>> Note that potential switching leads to errors in the lipid force field.
>> You need a buffered neighbor list with force switching.  The exact
>> parameters that you should use are listed on http://www.gromacs.org/
>> Documentation/Terminology/Force_Fields/CHARMM.  For lipids, you should
>> absolutely not deviate from these settings.  The protein and nucleic acid
>> force fields (and the remainder of CHARMM additive models) should use these
>> settings, though they are more forgiving (i.e. potential switching does not
>> lead to noticeable artifacts).  With lipids, the requirements are pretty
>> absolute.  People frequently report a drop in APL; every time they do, it's
>> because they're using the wrong settings.
>>
>> -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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>