[gmx-users] Splitted DMPC bilayer
Justin A. Lemkul
jalemkul at vt.edu
Tue Apr 5 00:27:16 CEST 2011
Dr. Ramón Garduño-Juárez wrote:
> Justin,
>
> Thank you for your comments after finishing the MD production run for up
> to 20 ns...
>
> Since this step was over very quickly, now I have a simple question
> ¿How long, in human time, should a production run last?
>
There is no way to answer that. It depends on the hardware, number of atoms,
system load, application of any number of the Gromacs algorithms, .mdp settings...
> The production run was carried out in six processors Intel Xeon (R)
> E5405 2.00 GHz. The last few lines of the md_0_1.log are:
>
> -----------------------------------------
> Parallel run - timing based on wallclock.
>
> NODE (s) Real (s) (%)
> Time: 180685.417 180685.417 100.0
> 2d02h11:25
> (Mnbf/s) (GFlops) (ns/day) (hour/ns)
> Performance: 232.900 12.351 9.564 2.510
> -----------------------------------------
>
> Is this correct? In my opinion it should lasted much more longer...
>
Nope, Gromacs is just fast :)
> Before reaching this point, this is an update of what we did...
>
> First we eliminated the SOL_SOL group and the only special index group
> was Protein_DMPC.
>
> Since the NVT equilibration failed, we took option # 2 of the "Advanced
> Troubleshooting", for the 1st phase of Equilibration.
>
> After this step we proceeded with the equilibration phase 2 with a 1-ns
> NPT equilibration which ended fine.
>
> Next, we proceeded with a 20 ns production run. Thus, the modified lines
> of the .mpd file found in the tutorial page were:
>
> nsteps = 10000000 ; 2 * 10000000 = 2000 ps (20 ns)
> tc-grps = Protein DMPC SOL
> comm-grps = Protein_DMPC SOL
>
> With this instructions the 20 ns simulation took 2d02h11:25
>
> I believe the "error" comes from the line
>
> constrains = all-bonds which surely must be changed to
>
> constrains = none or hbonds
>
Why do you say that? What error is occurring? You said your simulations were
running fine. You most certainly should not remove constraints if you're
sticking with a 2-fs timestep. The system will be unstable without constraints.
You might be able to get away with hbonds, but certainly not "none."
-Justin
> Looking forward to your comments...
>
> Much obliged,
> Ramon
>
> El 30/03/2011 12:25 p.m., Justin A. Lemkul escribió:
>>
>>
>> Dr. Ramón Garduño-Juárez wrote:
>>> Dear all,
>>> Dear Justin,
>>>
>>> This time I want to ask the gurus about this problem I encountered in
>>> the Equilibration step of my system made of 3 individual (small)
>>> protein chains in a solvated DMPC bilayer, no ions present since the
>>> protein system is neutral...
>>>
>>> Following the tutorial I started with
>>>
>>> make_ndx_d -f em_after_solv.gro -o index_after_solv.ndx
>>>
>>> for which I got the following list:
>>> -----------------------------------------------------------------
>>> Reading structure file
>>> Going to read 0 old index file(s)
>>> Analysing residue names:
>>> There are: 129 Protein residues
>>> There are: 123 Other residues
>>> There are: 3215 Water residues
>>> Analysing Protein...
>>> Analysing residues not classified as Protein/DNA/RNA/Water and
>>> splitting into groups...
>>>
>>> 0 System : 16649 atoms
>>> 1 Protein : 1346 atoms
>>> 2 Protein-H : 1025 atoms
>>> 3 C-alpha : 129 atoms
>>> 4 Backbone : 387 atoms
>>> 5 MainChain : 519 atoms
>>> 6 MainChain+Cb : 636 atoms
>>> 7 MainChain+H : 649 atoms
>>> 8 SideChain : 697 atoms
>>> 9 SideChain-H : 506 atoms
>>> 10 Prot-Masses : 1346 atoms
>>> 11 non-Protein : 15303 atoms
>>> 12 Other : 5658 atoms
>>> 13 DMPC : 5658 atoms
>>> 14 Water : 9645 atoms
>>> 15 SOL : 9645 atoms
>>> 16 non-Water : 7004 atoms
>>> -----------------------------------------------------
>>>
>>> Since I did not add ions I have formed a (merged) group named SOL_SOL
>>
>> Why would you merge solvent with itself?
>>
>>> after chosing 15 | 15 , and another merged group named Protein_DMPC
>>> by choosing 1 | 13...
>>>
>>> Next, I started the NVT equilibration with:
>>>
>>> grompp_d -f nvt.mdp -c em_after_solv.gro -p
>>> topol_mod_lip_solv.top -n index_after_solv.ndx -o nvt.tpr
>>>
>>> The nvt.mpd file is the same as the one given in the tutorial, the
>>> only changes I made were:
>>>
>>> tc-grps = Protein DMPC SOL_SOL
>>> and
>>> comm-grps = Protein_DMPC SOL_SOL
>>>
>>
>> I would think that using this weird SOL_SOL group would create
>> problems related to degrees of freedom, etc. If you have no ions,
>> there is no need to merge any sort of solvent-related groups.
>>
>>> After this I ran
>>>
>>> mdrun_mpi_d -v -deffnm nvt
>>>
>>> When this process is finished I looked at the resulting nvt.gro file
>>> and found the following:
>>>
>>> 1) The 3 protein chains complex is fine, at the center of the box as
>>> it should be, but
>>> 2) The 2 DMPC layer are separated (splitted) leaving a large gap
>>> between them forming a )( shape where the top and bottom of this
>>> figure contain one layer of DMPC plus water molecules, while in the
>>> narrow section the protein complex is found... In the void between
>>> the two DMPC layers no water molecules are present... Very odd!...
>>>
>>> Please advice...
>>>
>>
>> This is covered in the "Advanced Troubleshooting" section of my tutorial:
>>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/advanced_troubleshooting.html
>>
>>
>> -Justin
>>
>>> Cheers,
>>> Ramon Garduno
>>>
>>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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