[gmx-users] area per lipid

[Shima Arasteh]

Hi again,

I edited my md.mdp files. I'm wondering if my nvt.mdp and npt.mdp in charmm36 ff also need such a edition? 
Also I'd like to know if these mdp file are applicable in any simulation done with charmm36?



Sincerely,
Shima

________________________________
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com> 
Sent: Friday, November 9, 2012 3:49 PM
Subject: Re: [gmx-users] area per lipid



On 11/9/12 1:46 AM, Shima Arasteh wrote:
>
>
> I pick the snapshots every 10ns, because I don't know how much time this system needs to be simulated to reach to the proper APL.
>

What I'm saying is there are far better ways to assess any trends in your data 
rather than taking 4 snapshots along a much larger trajectory.  You can gather a 
lot more detail, and very easily.  You're saving snapshots every 2 ps, which 
means you will have 20000 data points that can be analyzed, rather than just 4.

> The md.mdp dile I used here is:
>
> title        = Production run for Water-POPC system
>
> ; Parameters describing the details of the NVT simulation protocol
> integrator    = md
> dt        = 0.002
> nsteps        = 5000000
>
> ; Parameters controlling output writing
> nstxout        = 1000
> nstvout        = 1000
> nstenergy    = 1000
> nstlog        = 1000
>
> ; Parameters describing neighbors searching and details about interaction calculations
> ns_type        = grid
> nstlist        = 5
> rlist        = 1.2
> rcoulomb    = 1.2
> rvdw        = 1.2
> pbc        = xyz
>

You're using a plain cutoff for the van der Waals interactions, which is 
incorrect for the CHARMM force fields.  You need the following:

vdwtype = switch
rvdw_switch = 0.8
rvdw = 1.2
rlistlong = 1.4

The other settings are fine.

-Justin

> ; Parameters for treating bonded interactions
> continuation    = yes
> constraint_algorithm = LINCS
> constraints    = all-bonds
> lincs_iter    = 1
> lincs_order    = 4
>
> ; Parameters for treating electrostatic interactions
> coulombtype    = PME
> pme_order    = 4
> fourierspacing    = 0.16
>
> ; Temperature coupling parameters
> tcoupl        = Nose-Hoover
> tc-grps        = POPC SOL
> tau_t        = 0.5    0.5
> ref_t        = 300     300
>
> ; Pressure coupling parameters
> pcoupl        = Parrinello-Rahman
> pcoupltype    = semiisotropic
> tau_p        = 2.0
> ref_p        = 1.0    1.0
> compressibility = 4.5e-5    4.5e-5
>
>
> DispCorr    = EnerPres
> gen_vel        = no
> nstcomm        = 1
> comm_mode    = Linear
> comm_grps    =POPC SOL
>
>
>
> Sincerely,
> Shima
>
>
> ________________________________
> From: Justin Lemkul <jalemkul at vt.edu>
> To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Friday, November 9, 2012 12:20 AM
> Subject: Re: [gmx-users] area per lipid
>
>
>
> On 11/8/12 4:39 AM, Shima Arasteh wrote:
>> Hi,
>>
>> I am trying to simulate POPC in water in 300 K, using charmm36 FF. In order to reach appropriate area per lipid ( 63-65 Angestroms per headgroup as mentioned in articles ), I let the system to be simulated for 40 seconds. To do so, I checked the area  per lipid every 10 ns. The results of area per lipid in each step are as below:
>>
>> 1.
>> Top leaflet: 60.44
>>
>> Bottom leaflet: 59.43
>>
>>
>> 2.
>> Top leaflet: 61.135
>> Bottom leaflet: 60.11
>>
>> 3.
>> Top leaflet: 61.40
>>
>> Bottom leaflet: 60.38
>>
>> 4.
>> Top leaflet: 60.27
>>
>> Bottom leaflet: 59.27
>>
>> I expected it to approaches the expected amount steadily, but why did I get such a result? How can I get to the appropriate area  per lipid?
>>
>> Would you please give me suggestions? Any suggestions would be appreciated.
>>
>
> Without seeing a complete .mdp file, it's hard to say.  Why are you picking
> snapshots every 10 ns?  You can easily plot APL over time for the entire
> trajectory using the box vectors stored in the .edr file from (Box-X *
> Box-Y)/(number of lipids).  You would have to write your own script to do the
> calculation, but it's quite straightforward.
>
> -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

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