[gmx-users] Splitted DMPC bilayer

Tue Apr 5 00:24:28 CEST 2011

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?

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...

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

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
>>
>
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