Re: [gmx-users] Box dimension

Perhaps a solution for those who don't like off-GROMACS topics, is to not get involved in such threads? ;) -- Viveca On Mon, Jun 4, 2018 at 9:07 AM, Alex wrote: > And again, your question has nothing to do with Gromacs. It has to do with > what you want to do, common sense, and basic

Re: [gmx-users] Bias potential during umbrella sampling

Hi Meena, No, they are not generally the same. The reaction coordinate using 'distance' is the norm of the COM distance vector (>=0). Using direction, it's the projection onto the given vector (possibly negative). -- Viveca On Fri, May 11, 2018 at 11:33 AM, Meena Singh

Re: [gmx-users] md simulation of circular rna

Hi, There is no direct support for generating the periodic topology in pdb2gmx, so that would require manually editing the topology/configurations of the end resiudes to connect them. -- Viveca On Sun, Apr 15, 2018 at 7:34 AM, Atila Petrosian wrote: > Dear all, >

Re: [gmx-users] Error when for gmx tune_pme on Cray

Thanks. It's running now. I just had a typo in my gmx_mpi variable that gave me the last error I posted. Using the non-mpi binary for tune_pme solved it. -- Viveca On Tue, Apr 10, 2018 at 5:22 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > On Tue, Apr 10, 2018 at

Re: [gmx-users] Error when for gmx tune_pme on Cray

uild, > and to let the default suffixing of the gmx binary handle itself so both > installations can go to the same place for convenience. > > Mark > > On Tue, Apr 10, 2018 at 3:50 PM Kutzner, Carsten <ckut...@gwdg.de> wrote: > > > Hi Viveca, > > > > >

[gmx-users] Error when for gmx tune_pme on Cray

Hi users, I never used gmx tune_pme before and thought I'd try. On a Cray machine, using aprun instead of mpirun, I did args="/cfs/klemming/nobackup/v/vivecal/programs/gromacs/2018.1/bin/gmx mdrun -pin on -quiet -stepout 5000 -ntomp 2 -noconfout" export MPIRUN=aprun; aprun -n 1 $gmx tune_pme

Re: [gmx-users] Speed up simulations with GROMACS with virtual interaction sites

Hi, There is this ancient gromacs page which I guess you already found: http://www.gromacs.org/Documentation/How-tos/Removing_fastest_degrees_of_freedom Here are a couple of references, the second for using virtual sites for CHARMM lipids: Bjelkmar, P., Larsson, P., Cuendet, M. A., Hess, B. &

Re: [gmx-users] Possible to extract gro file from a tpr?

ar option, genion with -conc 0. :) > > > > Alex > > > > > > On 3/30/2018 4:28 AM, Justin Lemkul wrote: > > > On Fri, Mar 30, 2018 at 5:38 AM Viveca Lindahl < > vivecalind...@gmail.com> > > > wrote: > > > > > >> Hi users, &

[gmx-users] Possible to extract gro file from a tpr?

Hi users, Is it possible to extract a gro file from a tpr? Unfortunately 'gmx mdrun -nsteps 0' does not give a confout.gro :) -- Viveca -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] source code for velocity information

Try posting in gmx-developers. -- Viveca On Wed, Mar 21, 2018 at 2:56 AM, 刘杰 wrote: > Dear all, Iam trying to add viscidity bond code to gromacsc 4.0.7. I > found the harmonic bond code in bondfree.c ,but i could not conform which > source document include the velocity

Re: [gmx-users] Replica Exchange Output control

Hi Akshay, What happens if you just try it? :) -- Viveca On Thu, Mar 15, 2018 at 12:43 PM, Akshay wrote: > Hello Gromacs Users, > > I am currently running T-REMD simulations with around 50-60 replicas. > Subsequent to simulations, I mostly use the lowest

Re: [gmx-users] Help with interpreting message for fatal error

wrote: > > > On 3/12/18 1:40 PM, Viveca Lindahl wrote: > >> Hi Justin, >> >> I'm using semi-isotropic pressure coupling and the periodicity is along >> z. I >> should say that I'm also adaptively biasing a base pair to open, which is >> triggeri

Re: [gmx-users] GMX 2018 and 'distance' pull

Hi Alex, If you think this is a bug introduced in gromacs 2018, perhaps you could file a bug report on https://redmine.gromacs.org/? Attaching tpr's (or run setups) both for the 2018 and the 5.04 version together with an md.log would be helpful. -- Viveca On Tue, Mar 13, 2018 at 7:38 AM, Alex

Re: [gmx-users] Help with interpreting message for fatal error

; a bit and would be as interested in understanding what is going wrong here, > although I have never encountered what you are observing. > > Best wishes, > > Gregory > > > > On 3/12/2018 7:42 AM, Viveca Lindahl wrote: > >> Hi Gregory, >> >> In th

Re: [gmx-users] Help with interpreting message for fatal error

to Berendsen coupling which avoids the problem (at least the fatal errors). -- Viveca On Mon, Mar 12, 2018 at 3:46 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/12/18 10:42 AM, Viveca Lindahl wrote: > >> Hi Gregory, >> >> In the sense that I see it hap

Re: [gmx-users] Help with interpreting message for fatal error

reproducible? > > Gregory > > > On 3/11/2018 7:30 AM, Viveca Lindahl wrote: > >> Hi, >> >> I'm running a simulation of a periodic DNA molecule. After some time I >> get, >> sometimes the following error message: >> >> --- >> >&g

[gmx-users] Help with interpreting message for fatal error

Hi, I'm running a simulation of a periodic DNA molecule. After some time I get, sometimes the following error message: --- A list of missing interactions: Proper Dih. of 3917 missing 1 Molecule type 'DNA_chain_A' the first 10 missing interactions, except for

Re: [gmx-users] Calculation of potential of mean force between sodium and chloride ion pair in water using replica exchange umbrella sampling in gromacs

Hi Mayank, Umbrella sampling replica exchange is currently not implemented in GROMACS. -- Viveca On Thu, Mar 8, 2018 at 5:32 PM, Mayank Dixit wrote: > Dear Gromacs Users, > I would like to calculate the potential of mean force between sodium and > chloride ion pair

Re: [gmx-users] Parmbsc1 force-field

; Best Regards, > > Dan > > On Mon, Mar 5, 2018 at 8:32 AM, Viveca Lindahl <vivecalind...@gmail.com> > wrote: > > > Hi Dan, > > > > I'm the author together (with Alessandra Villa). I hope it helps others > > providing the parameters on the website, but as M

Re: [gmx-users] Parmbsc1 force-field

Hi Dan, I'm the author together (with Alessandra Villa). I hope it helps others providing the parameters on the website, but as Mark said, it's up to you to double-check it. If you do find actual errors, I'm interested in hearing about it :) -- Viveca On Fri, Mar 2, 2018 at 5:19 PM, Dan Gil

[gmx-users] Example of arithmetic expression in gmx select?

Hi all, I'm trying to do selections that require addition, which is supposed to be supported according to 'gmx help selections'. I get syntax error however when doing from within 'gmx select': a=1+1 resid a What is the right syntax for achieving a=2...? Thanks, Viveca -- Gromacs Users mailing

Re: [gmx-users] pdb2gmx "dangling bond" error when trying to make periodically connected DNA

mented out. Viveca On Fri, Feb 2, 2018 at 5:21 PM, Viveca Lindahl <vivecalind...@gmail.com> wrote: > Hi, > > I'm trying to create a topology for DNA with periodically connected ends. > There's a previous message on this, with advice by Justin: > https://mailman-1.sys.kth.se/pip

[gmx-users] pdb2gmx "dangling bond" error when trying to make periodically connected DNA

Hi, I'm trying to create a topology for DNA with periodically connected ends. There's a previous message on this, with advice by Justin: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096970.html I have a single-stranded DNA structure in a pdb file with a phosphate on

Re: [gmx-users] tab completion gmx

you should see completion work in the same kind of way that git does. Mark On Tue, Sep 2, 2014 at 11:31 AM, Viveca Lindahl vive...@kth.se wrote: Hi all, Should I expect the tab completion of gmx to work (e.g. as with git)? Or is the idea to create aliases like g_energy='gmx energy

[gmx-users] tab completion gmx

Hi all, Should I expect the tab completion of gmx to work (e.g. as with git)? Or is the idea to create aliases like g_energy='gmx energy' for everything that I use? Viveca -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List