[gmx-users] Distance restraints

Dear All, I'm trying to keep distance restraints between few atoms, and for that I have done the following, In the topology file, I have inserted a block specifying the details of pairs -- ; Include forcefield

Re: [gmx-users] trajectory film

Hi Justin, Thank you very much! On Thu, Mar 12, 2015 at 9:53 AM, mah maz mahma...@gmail.com wrote: Dear all, I have a question probably not related to this mailing list! I want to see a film of an output trajectory via VMD. I tried the .trr file by the appropriate format in VMD, it shows

[gmx-users] cutting off the backbone bonds in polymer

Dear All, I am simulating a polystyrene melt with OPLS-AA force field. At the moment I am trying to cut off the bonds connecting styrene units on the chain backbone. Consequently, all the bond angles and dihedrals crossing these removed backbone bonds are also deleteted from the *.top file.

Re: [gmx-users] umbrella sampling tutorial

On 3/17/15 6:48 AM, Ming Tang wrote: Moring Justin, Many thanks to you. Sorry for the confused expression and the late reply. Today, I run the simulation step by step following the tutorial again. It turned out that the code you gave me recovers the behavior of the SMD portion of the

Re: [gmx-users] Normal mode analysis error

On 3/17/15 8:16 AM, rahul dhakne wrote: Dear all, I am trying to perform the Normal Mode Analysis protein in water. Here is the .mdp file I am using: integrator = nm; time step nsteps = 10 ; number of steps nstlist

[gmx-users] simulation of infinite chains

Dear gromacs users Previously, I simulated collagen triple helix chains, (GLY-PRO-HYP)n using Amber99sb-ILDN forcefield. When I processed pdb structures with pdb2gmx, I only obtained GLY in the N termini properly, and HYP was not processed(it was treated like HYP, not terminal HYP) since there

[gmx-users] DNA-protein complex

Hi, I am running MD for dsDNA-protein complex. After 50ns I observed that the DNA is unwinding. What did go wrong? Should I have changed something in my input file? Thank you in advance for your suggestions. best regards Urszula - Ta wiadomość została

Re: [gmx-users] Problem in making index.ndx and disres.itp

On 3/16/15 9:17 AM, Tushar Ranjan Moharana wrote: Hi Justine, As you can see in my .itp file the atom number starts from 1. Even this is the case with index file. I tried to modify index file to have atomic number same as pdb file but it gave a blank output. So my first concern is how GROMACS

Re: [gmx-users] Error while shrinking lipids (KALP15 in DPPC tutorial)

On 3/17/15 12:12 AM, Thomas Lipscomb wrote: Dear gmx-users, I am repeating the KALP15 in DPPC tutorial using Maximin 3 in DPPC using the CHARMM36 forcefield. I think the lipid shrinking was a step I did badly last time (I think I was getting can open em.tpr but not open em1.tpr, em2.tpr,

Re: [gmx-users] umbrella sampling tutorial

Moring Justin, Many thanks to you. Sorry for the confused expression and the late reply. Today, I run the simulation step by step following the tutorial again. It turned out that the code you gave me recovers the behavior of the SMD portion of the tutorial, and the problem is the distances.pl

Re: [gmx-users] DNA-protein complex

2015-03-17 14:35 GMT-03:00 Urszula Uciechowska urszula.uciechow...@biotech.ug.edu.pl: Hi, I am running MD for dsDNA-protein complex. After 50ns I observed that the DNA is unwinding. What did go wrong? Should I have changed something in my input file? You might want to send your input

Re: [gmx-users] Force field choosing and parameterization

Hi, Leandro Thanks for your explanation and tips. It helped me a lot. Initially, I'll try to do the parameterization for the fluorophore and substrate using GAFF and Antechamber, and then combine it with the AMBER forcefield. After that, I'll apply this new forcefield to carry out the MD

[gmx-users] jump problem

Dear users, I tried to remove the jumps of a structure after simulation but I couldn't do it. The structure is heterodimer. I tried the following ways: 1) -gmx trjconv -f md.xtc -s md.tpr -o traj_nojump.xtc -pbc nojump -gmx trjconv -f traj_nojump.xtc -s md.tpr -o traj_center.xtc -pbc mol -ur

Re: [gmx-users] umbrella sampling tutorial

Hi Justin, Thanks a lot. I can move forward now. Recently, I am trying to pull a triple helix, and want to fix the center of mass of the three terminal atoms. One paper said that it can be done by means of a strong harmonic restrain with a super large spring constant in Gromos96 53 a6. But I

Re: [gmx-users] umbrella sampling tutorial

Yes, it can not run. But I can extract the COM of different conf.groone by one manually. Due to the time difference, I will update the error message when I get to the office. Thanks. Sent from my Huawei Mobile Justin Lemkul jalem...@vt.edu wrote: On 3/17/15 6:48 AM, Ming Tang wrote: Moring

Re: [gmx-users] umbrella sampling tutorial

Hi Justin, Here is the error message. tm@tm-HP-Z420-Workstation:~/umbrella$ perl distances.pl Bareword found where operator expected at distances.pl line 8, near gmx distance -n index.ndx -s pull.tpr -f conf${i}.gro -select 'com of group Chain_A (Missing operator before Chain_A?) String

Re: [gmx-users] umbrella sampling tutorial

On 3/17/15 8:08 PM, Ming Tang wrote: Hi Justin, Here is the error message. tm@tm-HP-Z420-Workstation:~/umbrella$ perl distances.pl Bareword found where operator expected at distances.pl line 8, near gmx distance -n index.ndx -s pull.tpr -f conf${i}.gro -select 'com of group Chain_A

Re: [gmx-users] Forcefield parameters for Zinc

Hi, Related to the Zn-parameters; where can I find the reference (author, journal, year) to the sigma and epsilon (1.95998e-01 5.23000e-02) parameters that I find in /gromacs/top/amber99sb.ff/ffnonbonded.itp for [ atomtypes ] Zn. I would like to use amber99sb force field in my

[gmx-users] distribution of water molecules in system

Dear Gromacs Users, I want to show distribution of water inside the peptide based cylindirical nanofiber. To do this: 1) I created an index file which contains OW atoms (=Oxygen atoms belongs to the water molecules) 2) Then, I used the following command: g_rdf -f traj.xtc -s OW.ndx -o

[gmx-users] Normal mode analysis error

Dear all, I am trying to perform the Normal Mode Analysis protein in water. Here is the .mdp file I am using: integrator = nm; time step nsteps = 10 ; number of steps nstlist = 10; update