[gmx-users] Semiisotropic pressure coupling
shivangi.nangia at gmail.com
Fri Feb 13 04:34:34 CET 2015
> 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 1 [file md.mdp, line 78]:
Invalid enum 'force-switch' for variable vdw-modifier, using
Next time use one of: 'Potential-shift-Verlet' 'Potential-shift' 'None'
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?
Thanks in advance.
On Thu, Feb 12, 2015 at 10:30 PM, shivangi nangia <shivangi.nangia at gmail.com
> 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,
>> 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
>>> 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
>>> 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
>>> 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 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
>> Gromacs Users mailing list
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