[gmx-users] problem in energy minimization of the inflted system

[Mark Abraham]

On 28/03/11, Parul tew  <parultew at gmail.com> wrote:
> Dear GMX users,
> 
>  I am facing problem while doing energy minimization of the inflated system of a protein with membrane. I inflated the system and updated the removed lipids in the topology file. Now I am stuck during the energy minimization state. Below is the .mdp file for minimization.
> 
> 
> 
> ---------------------------------------------------------------------
> 
> 
> 
> ; minim_1.mdp - used as input into grompp to generate em_1.tpr
> 
> 
> integrator  = cg        ; Algorithm (cg = conjugate gradient minimization)
> 
> 
> 
> emtol       = 1000.0    ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
> 
> 
> 
> emstep      = 0.01      ; Energy step size
> 
> 
> 
> nsteps      = 50000     ; Maximum number of (minimization) steps to perform
> 
> 
> 
>  
> 
> 
> nstlist     = 1         ; Frequency to update the neighbor list and long range forces
> 
> 
> 
> ns_type     = grid      ; Method to determine neighbor list (simple, grid)
> 
> 
> 
> rlist       = 1.2       ; Cut-off for making neighbor list (short range forces)
> 
> 
> 
> coulombtype = PME       ; Treatment of long range electrostatic interactions
> 
> 
> 
> rcoulomb    = 1.2       ; Short-range electrostatic cut-off
> 
> 
> 
> rvdw        = 1.2       ; Short-range Van der Waals cut-off
> 
> 
> 
> gen_vel     = yes
> 
> 
> 
> 
> 
> 
> define      = DSTRONG_POSRES
> 
> 
> 

Your "define" line is wrong. Computers are very exact and you need to be also if you want to succeed at complex computational projects. Go and read in the documentation what the recommended define is.


> 
> 
> when I run this using the command 
> 
> 
> grompp –f minim_1.mdp –c system_inflated.gro topol.top –o em_1.tpr
> 
> 

This is not the line you should be using - you have no flag before "topol.top". However that's also not a problem.


> 
> 
> it generates the em_1.tpr file but does not generate any md_out.mdp  file and it gives the following 2 notes 
> 
> 

Unless you've used "grompp -po md_out.mdp" then the default filename is "mdout.mdp". You need to take care to get all this "punctuation" correct. A few seconds of being careful and methodical can save weeks of pulling out your hair...


> 
> 
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
> 
> 
> 
> 
> 
> checking input for internal consistency...
> 
> 
> 
> 
> 
> processing topology...
> 
> 
> 
> 
> 
> NOTE 1 [file topol.top, line 24414]:
> 
> 
> 
> 
> 
>   System has non-zero total charge: 1.400002e+01
> 
> 
> 
> 
> 
>   processing coordinates...
> 
> 
> 
> 
> 
> double-checking input for internal consistency...
> 
> 
> 
> 
> 
> Reading position restraint coords from system_inflated.gro
> 
> 
> 
> 
> 
> renumbering atomtypes...
> 
> 
> 
> 
> 
> converting bonded parameters...
> 
> 
> 
> 
> 
> initialising group options...
> 
> 
> 
> 
> 
> processing index file...
> 
> 
> 
> 
> 
> Analysing residue names:
> 
> 
> 
> 
> 
> Opening library file /usr/local/Gromacs/share/top/aminoacids.dat
> 
> 
> 
> 
> 
> There are:   121      OTHER residues
> 
> 
> 
> 
> 
> There are:   408    PROTEIN residues
> 
> 
> 
> 
> 
> There are:     0        DNA residues
> 
> 
> 
> 
> 
> Analysing Protein...
> 
> 
> 
> 
> 
> Analysing Other...
> 
> 
> 
> 
> 
> Making dummy/rest group for T-Coupling containing 9931 elements
> 
> 
> 
> 
> 
> Making dummy/rest group for Acceleration containing 9931 elements
> 
> 
> 
> 
> 
> Making dummy/rest group for Freeze containing 9931 elements
> 
> 
> 
> 
> 
> Making dummy/rest group for Energy Mon. containing 9931 elements
> 
> 
> 
> 
> 
> Making dummy/rest group for VCM containing 9931 elements
> 
> 
> 
> 
> 
> Number of degrees of freedom in T-Coupling group rest is 29790.00
> 
> 
> 
> 
> 
> Making dummy/rest group for User1 containing 9931 elements
> 
> 
> 
> 
> 
> Making dummy/rest group for User2 containing 9931 elements
> 
> 
> 
> 
> 
> Making dummy/rest group for XTC containing 9931 elements
> 
> 
> 
> 
> 
> Making dummy/rest group for Or. Res. Fit containing 9931 elements
> 
> 
> 
> 
> 
> Making dummy/rest group for QMMM containing 9931 elements
> 
> 
> 
> 
> 
> Checking consistency between energy and charge groups...
> 
> 
> 
> 
> 
> Calculating fourier grid dimensions for X Y Z
> 
> 
> 
> 
> 
> Using a fourier grid of 216x216x55, spacing 0.119 0.119 0.120
> 
> 
> 
> 
> 
> Estimate for the relative computational load of the PME mesh part: 0.96
> 
> 
> 
> 
> 
> NOTE 2 [file aminoacids.dat, line 1]:
> 
> 
> 
> 
> 
>   The optimal PME mesh load for parallel simulations is below 0.5
> 
> 
> 
> 
> 
>   and for highly parallel simulations between 0.25 and 0.33,
> 
> 
> 
> 
> 
>   for higher performance, increase the cut-off and the PME grid spacing
> 
> 
> 
> 
> 
> 
> This run will generate roughly 116 Mb of data
> 
> 
> 
> 
> 
> writing run input file...
> 
> 
> There were 2 notes
> 
> 
> gcq#22: "I Had So Many Problem, and Then I Got Me a Walkman" (F. Black)
> 
> 
> ------------------------------------------------------------------------------------------I understand the note 1 as I haven’t added the ions yet, so the system has charge.
> 
> 
> 
> But I am confused about note 2, what changes can I make to .mdp file for the minimization to run smoothly.
> 
> 

Is the minimization going to run in parallel, or for more than an hour? If not, who cares about parallel performance?

Mark
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110328/34933a18/attachment.html>