[gmx-users] gromacs.org_gmx-users Digest, Vol 170, Issue 27
jalemkul at vt.edu
Wed Jun 6 15:28:59 CEST 2018
On 6/6/18 2:12 AM, Muthukumaran Rajagopalan wrote:
> thank you for the reply Justin.
> though the APL looks close to the acceptable range, I am afraid the SN1 and SN2 acyl chain parameters are not in the range as reported by Pluhackova, K et al J. Phys. Chem. B 2016, 120, 3888?3903 and also the membrane thickness increases.
Increasing thickness and decreasing APL are physically linked, so that
What "range" of values are you getting, and how much do they differ?
What is the error bar? There's only one relevant plot in the paper you
reference, so it's hard to tell from a simple qualitative comparison
with no error bars.
Also note that your .mdp file posted yesterday was set to 310 K, the
published work was 308 K. While I don't expect a big difference, note
that you're not doing a truly apples-to-apples comparison.
Your .mdp settings are correct. The published paper makes no reference
to the switching scheme used, other than to say that Verlet is
equivalent to a switching function (which is far too vague for my
liking) so you should attempt to get input files from the corresponding
author to verify that the approaches are the same. CHARMM lipid
parameters absolutely require a force-switch, which some people neglect
to do properly.
>> Message: 3
>> Date: Tue, 5 Jun 2018 19:08:45 -0400
>> From: Justin Lemkul <jalemkul at vt.edu>
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] mdp-settings for charmm36 and lipid apl
>> Message-ID: <8f727384-96db-e744-73b8-b1f2bbe718ff at vt.edu>
>> Content-Type: text/plain; charset=utf-8; format=flowed
>> On 6/5/18 1:03 PM, Muthukumaran Rajagopalan wrote:
>>> Dear Gromacs Users,
>>> I have recently started performing membrane simulations in gromacs 5.01 version, I have started running simulations with pure POPE bilayer constructed from charmm-gui membrane builder with XY dimension 70 angs (84 lipids in each bilayer). The bilayer is solvated with 0.15 mol of KCL ( as Na ions have problem with lipid layers). The lipid layer is solvated with hydration number of 36 (lipid:water ratio).
>>> I went through a series of literature and gromacs mailing list regarding decrease in area per lipid and tried different combinations but the area per lipid decreases by 3-4 angs from the experimental values (~58 for POPE).
>>> I have referred Pluhackova, K et al J. Phys. Chem. B 2016, 120, 3888?3903
>> The APL value they obtained was 55.5 A^2, so your observations are
>> consistent. The force field apparently underestimates APL slightly.
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>> jalemkul at vt.edu | (540) 231-3129
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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