[gmx-users] coarse grain in gromacs

Hi, all: Has anyone done the coarse graining using MARTINI force field? Could you give me any suggestion on how to build a coarse grained model from the AA system? I checked the website(http://md.chem.rug.nl/~marrink/MARTINI/Coordinates.html ) and it seems to me they only provide a scrip

Re: [gmx-users] peptide goes out of box after md simulation

Bhawana Gupta wrote: hello everyone, After doing md simulation with no. of steps 1 ns ,my peptide which is of 7-8 residue move out of the boundary of water box. tell me what shd i do get rid of this problem. See http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions Also i want to

[gmx-users] peptide goes out of box after md simulation

hello everyone, After doing md simulation with no. of steps 1 ns ,my peptide which is of 7-8 residue move out of the boundary of water box. tell me what shd i do get rid of this problem. Also i want to know about the wall of the box, whether it is permeable or semi-permiable. this is very silly q

Re: [gmx-users] average radius of gyration

Q. Y. HUAN wrote: Dear all, I did g_gyrate and I obtained a gyration graph, then i did g_analyze with the following command: g_analyze -f gyration.xvg -av Then I obtained a set of values as follow: Read 4 sets of 201 points, dt = 10 std. dev.relative

[gmx-users] average radius of gyration

Dear all, I did g_gyrate and I obtained a gyration graph, then i did g_analyze with the following command: g_analyze -f gyration.xvg -av Then I obtained a set of values as follow: Read 4 sets of 201 points, dt = 10 std. dev.relative deviation of

Re: [gmx-users] ligand protein complex with ffamber99

Ragnarok sdf wrote: I am trying to setup a simulation with a ligand and a protein using ffamber99 forcefield. I have already generated the ligand's topology file using acpypi and everything seems to be all right in the files generated. However, while following the steps in the drug enzyme tuto

RE: [gmx-users] problem with distance restraints

Yes, the index is the residue number that you can take from the pdb file and the numbers for the atom pairs can be taken from the pdb or from the topology file. I must have a script that do this work from the pdb... if you are interested I could look for it (tomorrow). To understand the numbers yo

[gmx-users] Re: How long should I run a free energy simulation

Hi, I did a little test and I answered myself to the previous question. I changed the size of the chain for the calculation of the average of dH / dlambda (in this case I used a lambda of 0.56). I did time average ranging from 5 to 800ps and it seems that convergence is achieved in 500ps. I show th

[gmx-users] ligand protein complex with ffamber99

I am trying to setup a simulation with a ligand and a protein using ffamber99 forcefield. I have already generated the ligand's topology file using acpypi and everything seems to be all right in the files generated. However, while following the steps in the drug enzyme tutorial provided in the grom

RE: [gmx-users] problem with distance restraints

Thanks for the fast reply! So the index is the residue number, and I can get that from the pdb file right? And the numbers for the atom pairs, I'm assuming, should be coming from the topology file. But for each atom pair, should the low up1 and up2 columns always be equal to 0.0, 0.3, 0.8? Why is l

RE: [gmx-users] problem with distance restraints

You do not need so many distance restraints, it is enough to restraint the distance between the "O" atom of residue "i" and the "H" atom of the residue "i+4". Once you have the index for those atoms your [distance_restraints] section will have one of these lines ai aj 1 i 1 0.0 0.3 0.8 1