Re: [gmx-users] missing of methyl at N-terminal

I have had trouble capping N- and C- terminal residues using the 3.3.X series of GROMACS. I even think I started a thread about it. Before you digg that thread up you should: i) work out what you want to do ii) understand what result you should get iii) do it and check it !!! If that fails I s

Re: [gmx-users] ff53b6 for GROMACS 3.3.X?

Thanks for your response Berk. I have never heard of GROMOS 53b6. Does it exist? Yes it does. I have a pdf with parameters for GROMOS 53A6 and GROMOS 53B6 (vacuo). After attempting to locate the source it appears to be distributed to us (the pdf) when someone from Zurich was visiting. I'll

[gmx-users] ff53b6 for GROMACS 3.3.X?

Hi, I'm wondering ff53b6 is available with GROMACS or if anyone has it or is the a script available to convert the GROMOS FF to the required setup for use in GROMACS? I'm doing some development work in vacuum. Cheers Mitch ___ gmx-users mailing li

Re: [gmx-users] modify the distance constraints force constant during the simulation

I believe so, Could you not restart the simulation with grompp giving a modified .mdp file with the changed disres force constant? grompp - f NEW_MDP_WITH_DIFF_FC.mdp -c structure_out_after_previous_fc.gro -p top.top -t trajectory_at_previous_fc.trr -e energy_at_previous_fc.edr Cheers Mit

Re: [gmx-users] how to control temperature

You can do this with simulated annealing which is implemented in gromacs. See the simulated annealing section in the manual. Cheers Mitch Rui Li wrote: Hi all, I want the temperature is gradually increased by heating from 0 to 300 K for the first 20 ps, and then it is kept at 300 K for the n

Re: [gmx-users] Problem with using distance restraints (disre) with PBC

in a much larger system (as it is in my case) then it may be more suitable to modify the source code to avoid increasing the size of the system simulated. Tom --On Thursday, March 06, 2008 11:52:01 +1000 Mitchell Stanton-Cook <[EMAIL PROTECTED]> wrote: I have had a similar problem

Re: [gmx-users] Problem with using distance restraints (disre) with PBC

I have had a similar problem with orientation restraints. Are the residues far is space? Are you getting inconsistent shifts? If so - If so re-define your box size so that the shortest box vector is greater than the distance restraint residue + some tolerance. I also noticed - [ distance_res

Re: [gmx-users] Problem with amidation in pdb2gmx

Yeah. I select none for the terminal residues. Gromacs was compiled by myself. I have used this version in production runs for the last 5 months. Cheers Mitch Justin A. Lemkul wrote: Sorry, clicked 'send' too soon. How was this version of Gromacs compiled? I remember submitting a bugzilla

Re: [gmx-users] Gff53a6.rtp error (at least GMX331)

It has been pointed out that as an improper is defined (planar group) explicit inclusion of the third angle is not necessary. Mitch Mitchell Stanton-Cook wrote: Hi, I believe the ACE definition in ffG53a6.rtp is incorrect - Currently: [ angles ] CA C+Nga_19 O C+N

[gmx-users] Gff53a6.rtp error (at least GMX331)

Hi, I believe the ACE definition in ffG53a6.rtp is incorrect - Currently: [ angles ] CA C+Nga_19 O C+Nga_33 What I believe it should be - [ angles ] CA C Oga_30 CA C+Nga_19 O C+Nga_33 Cheers Mitch __

Re: [gmx-users] Inconsistent shifts.

consistent shifts? Cheers Mitch David van der Spoel wrote: Mitchell Stanton-Cook wrote: I have performed a search of the archive, but am yet to understand the meaning of "inconsistent shifts". I am using GMX331. I am simulating a protein structure solved by NMR. I have performe

[gmx-users] Inconsistent shifts.

I have performed a search of the archive, but am yet to understand the meaning of "inconsistent shifts". I am using GMX331. I am simulating a protein structure solved by NMR. I have performed EM, PR and run the structure out for 500ps of MD before beginning my production runs. I am using bo

[gmx-users] 3.3.2 mdrun problems

Dear all, I have been running GMX331. Recently I have encountered a documented restraint problem: "More than 8 graph edges per atom". See: * http://www.gromacs.org/pipermail/gmx-developers/2007-March/002060.html * http://www.gromacs.org/pipermail/gmx-developers/2006-April/001591.html Rather

Re: [gmx-users] grompp atomtype problem

This may be the case. However if not, I suggest you use the PRODRG beta server (top right hand corner on the main page) to produce output files for a more appropriate forcefield. I have generated and used files successfully using the beta server in the ff43a1. Cheers Mitch John E. Kerriga

Re: [gmx-users] Where to start ? Gmx Newb !!

You appear to have found this mailing list fine. I would suggest the gromacs manual on the gromacs website. This provides an introduction to MD topics and theory. This manual also provides references for literature of both historical and general importance in the field. There are plenty of t