[gmx-users] g_energy - what is COMPull En

Dear Gromacs users, I did pulling simulation and found COMPull En to give major contribution to my potential Energy, EPot. What is calculated by COMPull En? Thanks a lot in advance, Ilona Baldus -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx

Re: [gmx-users] Mix two solvents

Use the same box size for both. Then move one box with eidtconf -translate by its boxlength. Afterwards, you can simply put the boxes together to one large one. Quoting tekle...@ualberta.ca: Dear Gromacs, I want to combine two separately equilibrated solvents into one mixed solvent file.

Re: [gmx-users] Force output

I think this one can help you: http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000306 You can download a code that gives you the forces from the following website: http://projects.eml.org/mbm/website/fda_gromacs.htm Ilona Quoting Avisek Das : Dear GROMACS developers an

Re: [gmx-users] make ghost atom

I'm not sure if this helps, but have you tried link/ dummy atoms like you use them for QMMM? For dummies add a line to ff***nb.itp where you define them to have neither charge nor weight (also 0 for LJ-pot). Then add them to your topology-file. Check out http://www.gromacs.org/Documentation

Re: [gmx-users] Gromacs with QMMM Support

yes, that's right ;) Quoting Jack Shultz : I am reading this page http://wwwuser.gwdg.de/~ggroenh/qmmm.html Is it correct to assume you need one of the following to compile Gromacs with QMMM support? Gaussian GAMESS-UK MOPAC7 or mopac7.tar.gz -- Jack http://drugdiscoveryathome.com http://hy

[gmx-users] gromacs with gaussian 09

Hello, Has anyone amongst you tried if the Gaussian implementation also works for Gaussian 09? We were considering to get it, but it only makes sense for us if we can use it for Gromacs-Gaussian qmmm calculations. Have you experienced any other obstacles than variables being renamed? Chee

[gmx-users] 6-31G** for Gromacs

Hi Gerrit, I would like to use 6-31G** for my QMMM-calculation. Since sulfur is part of my QM system, I consider that a sensible thing to do. Unfortunately, it is not implemented in Gromacs, so I tried to add that bit myself. Here's the point where I got stuck: src/mdlib/qm_gaussian.c

Re: [gmx-users] access code for qmmm

Orca is free for example. Apparently, there's an implementation for Gromacs. Please send flowers and chocolate directely to Villa Bosch, where I am working. You find the adress on the internet ;) Quoting Farzad Molani : Hi Ilona, I saw the web adress. unfortunetly we don't have gaussia

Re: [gmx-users] access code for qmmm

Hi Farzad, I neither installed nor compiled Gaussian so far but actually, I am intending to do so in near future. I found this link: http://wwwuser.gwdg.de/~ggroenh/qmmm.html#doc (scroll down to Gaussian03) Cheers, Ilona Quoting Farzad Molani : Hello, I'm going to study reactions mec

Re: [gmx-users] Freezing a molecule

Quoting Jennifer Williams : Hello, One quick questions... I have a structure for which I now want to freeze a portion. I already have a .top file where the entire structure is flexible (bond angles, stretches and torions defined). When freezing, do I need to delete all those bond stretches, a

Re: [gmx-users] Re: gmx-users Digest, Vol 64, Issue 17

to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Ilona Baldus MPI Stuttgart INF 276 69120 Heidelberg Tel.: 06221-5451268 ___ gmx-users mailing list

[gmx-users] QMMM settings

Dear Gerrit, I am using Gromacs/Gaussian for qmmm-calculations. From the manual I could only find the instructions for how to use qmmm the "normal way", i.e. fill in the mdp file, but I learned from other Gromacs users that adding additional keywords was possible. How? Where do I put them?

RE: [gmx-users] pullx.xvg Meaning of output?

users@gromacs.org >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> >> Please search the archive at http://www.gromacs.org/search >> before posting! >> >> Please don't post (un)subscribe requests to the list. Use the >> >> www

RE: [gmx-users] pullx.xvg Meaning of output?

___ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ Ilona Baldus MPI Stuttgart INF 276 69120 Heidelberg Tel.: 06221-5451268 ___ gmx-users mailing listgmx-us

[gmx-users] pullx.xvg Meaning of output?

Hi! I am trying to understand the output of my pulling simulation: I get a pullx.xvg file which shows 0Z, 1dZ, 2dZ after pulling in Z and -Z direction. I really cannot figure out the meaning of 1dZ and 2dZ. Since the website is down I cannot check on previous issues, so sorry for asking the

[gmx-users] pullx.xvg

Hi, Can anyone please tell me, what the output pullx.xvg actually shows? I used "System" as reference group while pulling in Z- and -Z-direction and the output legend shows 0 Z, 1 dZ, 2 dZ. I would have expected it means the reference group, and the distances to pull group 1 and two, but th

[gmx-users] maximum size for Freeze group?

Hi, I built an Argon box around my system that shall work as walls. Therefore all Argon atoms should be frozen. There are 33900 Argon atoms in my system but during grompp-ing the following message occurs: Making dummy/rest group for T-Coupling containing 62956 elements Making dummy/rest gr

[gmx-users] TIP5P - dummies sit on top of each other

Hi, I am trying to change my ice crystal from a three-site water model to the TIP5P water model. For that I use pdb2gmx. The program adds the two dummy atoms, but they are at exactly the same position as the oxygen and not two additional sites as stated by the paper and also as I find in

Re: [gmx-users] freeze group gives Segmentation fault

I just tried Gromacs 4.0.2. It still gives a Segmentation fault: "Reading file topol.tpr, VERSION 4.0.2 (single precision) Loaded with Money Segmentation fault" I did a test, putting the whole system into one freezegroup. Then the simulation starts running. But some of the atoms belonging to

[gmx-users] freeze group gives Segmentation fault

Hi! I am trying to use freezegroups on an ice-crystal. grompp gives no warning. Trying the same simulation but removing the freezegroup works. Please note my mdp-file's attached Ilona ; ; File 'mdout.mdp' was generated ; By user: bq_ibaldus (2417) ; On host: cln-fg06 ;