Re: Psf file generation with Gromacs Parameters

From: Fotis Baltoumas (fbaltoumas_at_biol.uoa.gr)
Date: Wed Nov 08 2017 - 17:43:42 CST

Hello Amali,

I may be wrong, but I think that many of the stuff that usually applies
to GROMACS topology files are not really functional in NAMD.

For one thing, I don't believe that multiple "grotopfile" arguments
work, you probably need to contain your topology in one single topol.top
file (similar to how you use one single psf file).

The "include" statements usually found in most topol.top GROMACS
topologies also may not be recognized.

The best thing you could do is compile a tpr file with gmx grompp as you
would normally do with GROMACS, and add the -pp flag during compilation;
this will produce a "processed" topology file which contains all
information relevant to your system without includes, i.e., atomtypes,
bondtypes etc. However, even that may require some additional tinkering
to be fully compatible with NAMD.

Finally, I see you're trying to use the GROMOS96 54A7 force field, which
- among other things - features a cosine functional form for the angle
potential instead of the harmonic one.  I can't say for certain whether
NAMD can actually model that correctly. There is a "cosAngles" option
that provides this functionality, however it was designed for Martini
coarse-grained simulations, and I don't know if it will work outside the
Martini mode.

Good luck,

Fotis

On 11/09/2017 01:17 AM, Amali Guruge wrote:
> Thank you very much for the answer. I tried to do the simulation, but
> again I got the following error.
>
> Charm++ fatal error:
> FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
>
> My em.conf file contains following parameters.
>
>
> #############################################################
> ## ADJUSTABLE PARAMETERS                                   ##
> #############################################################
>
> set inputname   PEG_SOL
> set current     em
>
> #structure          $inputname.psf
> #coordinates        $inputname.pdb
>
> # Set body temprature
> set temperature    298
> set outputname     ${inputname}_$current
>
> firsttimestep      0          #only necessary if not using catdcd
>
>
> #############################################################
> ## SIMULATION PARAMETERS                                   ##
> #############################################################
>
> # Input
> #paraTypeCharmm      on
> #parameters          top_prm/par_all36_cgenff.prm
> #parameters          top_prm/PEG.prm
> temperature         $temperature
>
> gromacs         on
> grotopfile          C12EO6.itp
> grotopfile        gromos54a7_atb.ff/spc.itp
> coordinates         structures/C12EO6_water_rbox.pdb
>
> # Force-Field Parameters (lowering settings adds error risk, current
> settings widely used)
> exclude             scaled1-4
> 1-4scaling          1.0
> cutoff              12.
> switching           on
> switchdist          10.
> pairlistdist        13.5
>
> # Integrator Parameters (only a few valid combinations, consult NAMD
> manual)
> timestep            2.0  # 2fs/step
> rigidBonds          all  # needed for 2fs steps
> nonbondedFreq       1
> fullElectFrequency  2
> stepspercycle       10
>
>
> # Constant Temperature Control
> langevin            on               # do langevin dynamics
> langevinDamping     5                # damping coefficient (gamma) of 5/ps
> langevinTemp        $temperature
> langevinHydrogen    off              # don't couple langevin bath to
> hydrogens
>
> # Periodic Boundary Conditions (start size of unit cell, ignored once
> .xst specified)
> cellBasisVector1    152.0  0.  0.
> cellBasisVector2    0.  152.0  0.
> cellBasisVector3    0.  0.  152.0
> cellOrigin          0.  0.  0.
>
> wrapWater        on
> wrapAll             on
>
>
> # PME (for full-system periodic electrostatics)
> PME            yes
> pmeGridSpacing        1.0
>
>
> # Constant Pressure Control (variable volume)
> useGroupPressure      yes     # needed for rigidBonds
>
> # yf for membrane simulations, should switch these on
> useFlexibleCell       yes
> useConstantRatio      yes    #keeps xy plane aspect ratio constant
> useConstantArea       no        #when yes volume is fixed, still
> allows stretching
>
> langevinPiston        on
> langevinPistonTarget  1.01325   #in bar -> 1 atm
> langevinPistonPeriod  100.
> langevinPistonDecay   50.
> langevinPistonTemp    $temperature
>
>
> # Output
> outputName          $outputname
>
> restartfreq         25000     # 500steps = every 1ps
> dcdfreq             30
> xstFreq             30
> outputEnergies      40     # must be multiple of stepspercycle
> outputPressure      40
>
>
> #############################################################
> ## EXTRA PARAMETERS                                        ##
> #############################################################
>
> # Interactive MD
> #IMDon on
> #IMDport 5678
> #IMDfreq 1       #update frequency, as low as bandwidth allows
> #IMDwait no      #if yes, job only runs while connected
>
> #############################################################
> ## EXECUTION SCRIPT                                        ##
> #############################################################
>
> minimize            5000
> reinitvels          $temperature
>
>
>
>
>
> On Tue, Nov 7, 2017 at 4:22 PM, Haohao Fu <fhh2626_at_gmail.com
> <mailto:fhh2626_at_gmail.com>> wrote:
>
> Hi Amail Guruge,
>
> NAMD can use gromacs files directly, see
> https://www-s.ks.uiuc.edu/Research/namd/2.12/ug/node14.html
> <https://www-s.ks.uiuc.edu/Research/namd/2.12/ug/node14.html>
>
> You can also try Parmed
> (http://parmed.github.io/ParmEd/html/index.html
> <http://parmed.github.io/ParmEd/html/index.html>) if you want to
> have psf and pdb files.
>
> Cheers,
> Haohao
>
> 2017-11-07 9:53 GMT+08:00 Amali Guruge <amaligg2010_at_gmail.com
> <mailto:amaligg2010_at_gmail.com>>:
>
> Dear NAMD users,
>
> I want to simulate my system considering Gromacs force field
> parameters. In that case how I generate the psf file? Can
> anyone help me?
>
> Thank you in advance.
>
>
>

-- 
*******************************************
Fotis A. Baltoumas
Phd Candidate, Bioinformatics Postgraduate Programme
Department of Cell Biology and Biophysics
Faculty of Biology, University of Athens
Panepistimiopolis, Athens 157 01, GREECE
   --------------------------------------
email : fbaltoumas_at_biol.uoa.gr
http://biophysics.biol.uoa.gr
http://bioinformatics.biol.uoa.gr
*******************************************

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