Re: [gmx-users] *.pdb file for the Tip4p/ice model

Thanks for a good idea. I am also doing the same. Sheelan S C Phys Chem Div From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Elton Carvalho [elto...@gmail.com] Sent: Monday, April

[gmx-users] Umbrella sampling without pull

Himy question is , can we use Umbrella Sampling without Pulling, Is it possible? i know the concept of Umbrella sampling and Replica Exchange, i have performed solvation of different small molecules in water and calculated energies. some of results are not good, so how can i improve these

Re: [gmx-users] position restraints

Thanks, I figured it out. (In case anyone wonders) the comma was not necessary: freezegrps = Protein-H YB freezedim = Y Y Y Y Y Y > On Apr 4, 2016, at 5:51 PM, Christopher Neale > wrote: > > I didn't use freezegrps in a long time, but I presume that you define a

Re: [gmx-users] position restraints

I didn't use freezegrps in a long time, but I presume that you define a group in the .ndx file and then you use the name of that group. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf

Re: [gmx-users] position restraints

Thanks, it worked! I couldn’t find anything in the documentation/manual as to how the groups to be freezed are named. For my case, I want to freeze the protein heavy atoms and ytterbium ions. In that case, would I do freezegrp = Protein-H, YB and freezedim = Y Y Y Y Y Y? Best, Irem > On

Re: [gmx-users] position restraints

I've never understood it, but when your system gets more complicated it is often necessary to use flexible water during minimization. define = -DFLEXIBLE for most water molecules. You can remove this for the MD, but it is for me sometimes necessary for EM. You have nearly unlimited options for

Re: [gmx-users] position restraints

I did, and I have a more specific question: what options do I have for specifying freeze groups? Right now I’m trying Protein-H. I also have a specific kind of ion that I’d like to freeze. The energy minimization step fails, as GROMACS complains that it can’t settle a water molecule (which is

Re: [gmx-users] position restraints

Check the manual for freezegrps ? ___ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Irem Altan Sent: 04 April 2016 15:54 To: gmx-us...@gromacs.org Subject: Re:

Re: [gmx-users] position restraints

Hi, The .mdp file is as follows: title = OPLS Lysozyme NVT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 5000 ; 2 * 5 = 10 ns dt =

Re: [gmx-users] position restraints

What did you set for refcoord-scaling ? How are you treating volume/pressure? Please post a full .mdp file. If you want, you can simply fix the positions and not let them move at all with freezegrps etc. From:

Re: [gmx-users] Restraints Riddle/Pull Puzzle

Possibilities that come to mind: (1) absolute position restraints (2) pull code distance restraints of each arm separately to the bottom of the U (3) put 2x U-shaped proteins in the same box. It takes longer to simulate, but you get twice the sampling (4) go back to the drawing board (this is

Re: [gmx-users] *.pdb file for the Tip4p/ice model

Since ice is a crystal, you can build a crystalline unit cell by hand (the unit cell will have one or two water molecules, so it's pretty easy to do it by hand, you just have to be careful to use the same atom ordering as the topology) and replicate it using gmx genconf so the crystal has the

[gmx-users] position restraints

Hi, I have a simulation in which I want to keep the protein coordinates fixed. I have tried using force constraints of strength 1000, 5000, and 1. With 5000, there are about 100-150 atoms (out of ~1700) that drift more than 0.4A away from their equilibrium positions. This number increases

[gmx-users] Restraints Riddle/Pull Puzzle

Okay, so... I have a U shaped protein and the diameter of the U is larger than half the shortest box vector. And it is already a huge box. I want to prevent the U from straightening out. My attempts at distance restraints fail because the shortest distance between the ends of the U is across the

Re: [gmx-users] on -dt of trjcat and trjconv

Dear Brett, MOD refers to the modulus operator. For example, trjconv -f infile.xvg -s infile.tpr -dt 1000 -o outfile.xvg will downsample a trajectory and save only the frames at multiples of 1000 ps (0 ps, 1000 ps, 2000 ps, …), assuming that infile.xvg starts at 0 ps. Kind regards, Erik > On