[gmx-users] gromacs.org_gmx-users Digest, Vol 170, Issue 27

[Justin Lemkul]

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 
makes sense.

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.

-Justin

>   
>
>>
>>
>>
>> ------------------------------
>>
>> 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
>> 	values
>> 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
>>
>> -- 
>> ==================================================
>>
>> 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
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
>>
>>
>>
>>

-- 
==================================================

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
http://www.thelemkullab.com

==================================================