[gmx-users] Re: how modify the forcefield amino acid definitions for non-naturally occuring amino acids?

Thank you Justin for your prompt reply, as usual :) With the last 2 lines of my previous post, I was referring on how to build *.itp files for completely new molecules (say lipids such as DMPC, DMPE or glutathione) that are not defined in the forcefield. I.e. how to derive dihedral angle code, for

[gmx-users] Re: Test particle insertion extra coordinate

Thank you so much for taking the time to look at the code. That should work, I will try it. -- View this message in context: http://gromacs.5086.n6.nabble.com/Test-particle-insertion-extra-coordinate-tp4536816p4546442.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. --

Re: [gmx-users] Re: Test particle insertion extra coordinate

The error is correct. After inspecting the code, the extra coordinate (coordinate of the cavity) is taken from the last atom of the trajectory (rerun_fr.x) and not from the .tpr file (mdatoms). This is weird, but allows different cavities for different frames I guess... I am guessing you can add t

[gmx-users] Re: Test particle insertion extra coordinate

Thanks a lot for the reply! I did as you said. I had a coordinate file where I wanted to add insert a water molecule withing a cavity. I added these lines to the .gro file: 340SOL OW 1274 2.925 0.061 2.677 0.2533 -0.1222 0.1294 340SOLHW1 1275 2.893 0.000 2.605 -0.1856 0.5

Re: [gmx-users] Re: Test particle insertion extra coordinate

Hello MPID (?), Sorry, I did not see your first message. For the tpic algorithm, the coordinate of insertion is the last coordinate (after the particle to be inserted) in the .tpr you give for the mdrun -rerun. Hence, you should create a structure file (.gro) with the original system, followed by

[gmx-users] Re: Test particle insertion extra coordinate

If no one knows this, does anyone know the best way to add a coordinate to a trajectory in general? -- View this message in context: http://gromacs.5086.n6.nabble.com/Test-particle-insertion-extra-coordinate-tp4536816p4546083.html Sent from the GROMACS Users Forum mailing list archive at Nabble.c

Re: [gmx-users] Amber99bsc0

It is possible but not yet included in Gromacs. As far as I know, there are several people working on porting this forcefield to Gromacs (I have been searching for this myself last year). Check the archives for parmbsc0 and Gromacs and search for papers that include these terms. then you will fi

Re: [gmx-users] how modify the forcefield amino acid definitions for non-naturally occuring amino acids?

Kirill Bessonov wrote: Dear Gmx users, I had been using Gromacs for couple of years and always found these forums quite helpful. Right now again I have another question to ask that I was not able to figure out yet myself and reading previous posts. I need to the ffG53a6 forcefield to be ab

Re: [gmx-users] Is TRO defined correctly in the ffG43a1p forcefield file?

Kirill Bessonov wrote: Dear all, I am trying to run simulation with phosphorylated Threonine (TRO) and I found lot's of info about this issue reading previous posts which explained on how to patch the force-field files and define this modified amino acid. After looking at the community forc

[gmx-users] Is TRO defined correctly in the ffG43a1p forcefield file?

Dear all, I am trying to run simulation with phosphorylated Threonine (TRO) and I found lot's of info about this issue reading previous posts which explained on how to patch the force-field files and define this modified amino acid. After looking at the community forcefield offered here http://www

[gmx-users] how modify the forcefield amino acid definitions for non-naturally occuring amino acids?

Dear Gmx users, I had been using Gromacs for couple of years and always found these forums quite helpful. Right now again I have another question to ask that I was not able to figure out yet myself and reading previous posts. I need to the ffG53a6 forcefield to be able to recognize the non-standa

Re: [gmx-users] Advice on High Precision Structure File Formats

Tot Ziens! Op 4 mar 2012 om 18:44 heeft "Andrew DeYoung" het volgende geschreven: > Hi, > > If you have time, I would be grateful for any advice you have about which > structure file format that I should use. I am attempting to create a carbon > nanotube. However, the carbon-carbon bond l

[gmx-users] Advice on High Precision Structure File Formats

Hi, If you have time, I would be grateful for any advice you have about which structure file format that I should use. I am attempting to create a carbon nanotube. However, the carbon-carbon bond length that I would like to use is 0.1415 nm, which means that I would like a structure file format

[gmx-users] Amber99bsc0

Hi! I want to use amber99bsc0 in gromacs. is it possible? thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscr

[gmx-users] Re: Gromacs-GPU benchmark test killed after exhausting the memory

Hi Szilard, Thanks for your reply. I used your script and I think it does look as a memory leak. Please look at the attached runchkmem.out Is it possible this problem exists in version 4.5.5 and was solved in version 4.6 you are using? When will version 4.6 be released? Thanks, Efrat >Messag

Re: [gmx-users] problem in using OPLS forcefield parameter in lipid simulation

On 4/03/2012 10:15 PM, Anushree Tripathi wrote: I am not getting the "ffoplsaanb.itp" file for lipid simulation.PLease tell me how to locate the file. It depends on your system and GROMACS version. See http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_i

[gmx-users] problem in using OPLS forcefield parameter in lipid simulation

I am not getting the "ffoplsaanb.itp" file for lipid simulation.PLease tell me how to locate the file. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before pos