[gmx-users] Splitted DMPC bilayer

["Dr. Ramón Garduño-Juárez"]

Justin,

Again much obliged for your comments. They are most illustrative...

I would like to make a final note on the issue of these many e-mails...

I am sure that GROMACS is fast, but that fast?...

For the sake of knowing that we are doing the right things, this is our 
topol.top file in which we eliminated all POSRES for the Protein and 
DMPC, not so for the WATER...
-------------
; Include forcefield parameters
#include "./gromos53a6_lipid.ff/forcefield.itp"

; Include chain topologies
#include "topol_Protein_chain_A.itp"
#include "topol_Protein_chain_B.itp"
#include "topol_Protein_chain_C.itp"

; Include water topology
#include "./gromos53a6_lipid.ff/spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
    1    1       1000       1000       1000
#endif

; Include topology for ions
#include "./gromos53a6_lipid.ff/ions.itp"

[ system ]
; Name
mod.pdb

[ molecules ]
; Compound        #mols
Protein_chain_A     1
Protein_chain_B     1
Protein_chain_C     1
----------------------

On Protein_chain_A  there are 342 atoms
On Protein_chain_B  there are 289 atoms
On Protein_chain_C  there are 715 atoms
On DMPC there are 123 molecules of 46 atoms each
On SOL there are 3205 molecules of 3 atoms each
For a total of 16619 atoms

I know that this is a medium size system for which I was expecting 
longer CPU time for a 20 ns MD run.

I know that there was no "error", which I meant is that I was surprised 
by the outcome...

May be GROMACS is as fast as it is claimed...

Cheers,
Ramon

El 04/04/2011 05:27 p.m., Justin A. Lemkul escribió:
>
>
> 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
>>
>
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