Re: Psf file generation with Gromacs Parameters

From: Amali Guruge (amaligg2010_at_gmail.com)
Date: Thu Nov 09 2017 - 19:45:28 CST

Dear NAMD users,

I included all parameters in one file; system.top and I removed the
"include" statements in it. When I tried to run the simulation, it gave the
following error.

Charm++ fatal error:
unexpected call to exit by user program. Must use CkExit, not exit!

In log file, the last line is
"USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS"
There is nothing beyond this statement.

If anyone familiar with this type of error, could you please guide me to
solve the problem.

Thank you.

On Thu, Nov 9, 2017 at 10:43 AM, Fotis Baltoumas <fbaltoumas_at_biol.uoa.gr>
wrote:

> 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> wrote:
>
>> Hi Amail Guruge,
>>
>> NAMD can use gromacs files directly, see https://www-s.ks.uiuc.edu/Rese
>> arch/namd/2.12/ug/node14.html
>>
>> You can also try Parmed (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>:
>>
>>> 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.grhttp://biophysics.biol.uoa.grhttp://bioinformatics.biol.uoa.gr
> *******************************************
>
>

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