[gmx-users] Acetonitrile with CHARMM ff

Sonia Milena Aguilera Segura sonia-milena.aguilera-segura at enscm.fr
Thu Jul 13 15:16:15 CEST 2017





----- Original Message -----
> From: "gromacs org gmx-users-request" <gromacs.org_gmx-users-request at maillist.sys.kth.se>
> To: "gromacs org gmx-users" <gromacs.org_gmx-users at maillist.sys.kth.se>
> Sent: Thursday, July 13, 2017 2:58:39 PM
> Subject: gromacs.org_gmx-users Digest, Vol 159, Issue 66
> 
> Send gromacs.org_gmx-users mailing list submissions to
> 	gromacs.org_gmx-users at maillist.sys.kth.se
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or, via email, send a message with subject or body 'help' to
> 	gromacs.org_gmx-users-request at maillist.sys.kth.se
> 
> You can reach the person managing the list at
> 	gromacs.org_gmx-users-owner at maillist.sys.kth.se
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
> 
> 
> Today's Topics:
> 
>    1. Error in simulating graphene (B S Bhushan)
>    2. Re: umbrella sampling (Justin Lemkul)
>    3. Re: Concrete pull code explanation needed (Justin Lemkul)
>    4. Re: ACETONITRILE with CHARM ff (Justin Lemkul)
>    5. Re: Non-periodic COM Pulling (Justin Lemkul)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Thu, 13 Jul 2017 15:33:16 +0530
> From: B S Bhushan <ecebhushan at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Error in simulating graphene
> Message-ID:
> 	<CAK60_SZ7Ev+JS5vevo5xJKOth1v0h3xM3gO7TzwmkOqGtzk3Lw at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
> 
> Dear Experts,
> 
> I am new to gromacs. I want to simulate electric double layer capacitance
> at graphene - liquid electrolyte interface. so far, I have practiced the
> tutorials from bevanlab page "Lysozyme in water" "biphasic systems". Next,
> I was trying to simulate the CNT/graphene tutorials available at thirdparty
> web pages. However I am getting errors while trying to generate topology
> file using *x2top* module.
> 
> When following the tutorial given at
> http://chembytes.wikidot.com/grocnt#toc
> I am getting the error,
> "*Inconsistency in user input:*
> *Could not find force field 'cnt_oplsaa' in current directory, install tree
> or*
> *GMXLIB path*."
> 
> 
> When following the tutorial given at
> http://machine-phase.blogspot.in/2009/04/single-wall-carbon-
> nanotubes-in-403.html
> I am getting the error,
> "*Fatal error:*
> *Could only find a forcefield type for 0 out of 168 atoms.*"
> 
> 
> Please suggest.
> Thank you so much for your time and knowledge.
> 
> 
> 
> 
> Awaiting suggestions,
> B S Bhushan
> Research Scholar,
> ABV - Indian Institute of Information Technology and Management, Gwalior,
> India.
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Thu, 13 Jul 2017 08:56:14 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] umbrella sampling
> Message-ID: <995aa507-8875-8c41-674b-84eded63e834 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed

> > 
> > Dear Justin,
> > 
> > I increased the size of the simulation box to 4 nm. Indeed, the values of
> > pressure improved (averages around -1 bar or 1.5, 2 bar, or so). However,
> > the T keeps being overestimated (302 K). During NVT I got the right value,
> > so I decided to run the 200 ns NPT equilibration with Berendsen barostat
> > instead of P-R. I got the right T value, around 298.3 and a pressure of
> > 1.5 more or less. Then I launched a continuation test with 200 ps MD with
> > P-R (I couldn't use the -e option because it gives me the error Could not
> > find energy term named 'Box-Vel-XX', moreover, I didn't use P-R before so
> > I guess I shouldn't expect stored values for it?. But I am using -t ).
> > Despite I got low pressure averages around 0.5 bar, the temperature raised
> > again to 301-302. This happens very early in the simulation, which seems
> > to indicate that for sd integrator/thermostat and P-R barostat there is
> > something going on. I am getting practically the same density in between
> > simulation, so I guess I can say t
>  ha
> >   t in term of P, the system has been equilibrated. However, what can I do
> >   to get the right T for this system? If I was able to get the right T
> >   with Berendsen barostat, I don't understand what's wrong when I change
> >   to P-R.
> > 
> 
> Sounds buggy.  What version of GROMACS are you using?  There were temperature
> issues with the Langevin integrator in previous versions, but those should
> have
> been long since solved.

I am using version 5.1.2. I checked the release notes for version 5.1.3 and 5.1.4 and the only thing related with sd integrator (none) or P-R barostat is this one 'Fixed Parrinello-Rahman with nstpcouple > 1'. Can this be the cause? 

Thank you.
> 
> -Justin
> 


More information about the gromacs.org_gmx-users mailing list