[gmx-users] QMMM install on GMX5.1

Hi all, Does anyone know how to install qmmm code like mopac to gmx5.1? Best, Xianchi -- 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 http://www.gromacs.org/Support/Mailing_Lists * For

Re: [gmx-users] Free energy change and volume of the box

Hi Alex, The free energy does depend on volume Thus, you should simulate bound and free state with the same volume. However, this is not necessary, since the error is pretty small usually (in my experience) Here two references: H?nenberger, Philippe H., and J. Andrew McCammon. "Effect of

Re: [gmx-users] trr file

Hello Rita, I think the answer is trjconv. Try to convert it to xtc, reduce the number of frames (with dt or skip), or reduce the components on the trajectory. If you don't need solvent for the calculations you can create a trajectory without it. Removing the solvent and convert it to xtc should

Re: [gmx-users] trr file

Hi Rita, You should be able to use analysis tools on an xtc file instead. Storage-wise you could also just have an xtc. For restarting if any files are missing they should all be missing except the cpt. You can rename or move the rest rather than deleting them though. Best wishes James > Dear

[gmx-users] trr file

Dear all, Probably a rookie question but anyone knows how to reduce trajectory volume file to be analyzed (I have already tried trjconv)? I have a trr file with 167 GB and analysis tools crash. Thanks, Rita. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Free energy change and volume of the box

Have you had a look at http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme to see if that technique would be applicable to you and look through the references given? When you do absolute transformations you will need to think about standard state

Re: [gmx-users] trr file

Hello, Thank you for your suggestions. I have already tried run trjconv but, as trajectory is heavy and server is full, out of memory error appears and analysis tool crash. Best, Rita. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se

Re: [gmx-users] trr file

Hi I think you can try analysis in more than one step by using -b and -e option of trjconv. On Fri, Oct 14, 2016 at 5:59 PM, Mark Abraham wrote: > Hi, > > Prevention is the best medicine - ask google about reducing GROMACS > trajectory storage volume :-) > > Mark > >

Re: [gmx-users] trr file

Have you tried the option -split? I never tried, and I don't know if it will solve your problem, but give it a try. On Fri, Oct 14, 2016 at 11:34 AM, Rita Paiva Melo < ritam...@ctn.tecnico.ulisboa.pt> wrote: > Hello, > > Thank you for your suggestions. I have already tried run trjconv but, as >

Re: [gmx-users] trr file

Hi, Prevention is the best medicine - ask google about reducing GROMACS trajectory storage volume :-) Mark On Fri, Oct 14, 2016 at 1:20 PM Nuno Azoia wrote: > Have you tried the option -split? > I never tried, and I don't know if it will solve your problem, but give it > a