[gmx-users] Fwd: Fw: Confusion about itp file generated by topolbuild

Hi all, I tried to generate topology file for benzene (as a trial) using topolbuild1_3. The itp file generated is (ffben.itp in my case) #define _FF_GAFF #define _FF_AMBER #define _FF_USER [ defaults ] ;nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2

[gmx-users] Fw: Confusion about itp file generated by topolbuild

On Tuesday, June 3, 2014 4:55 PM, Bikramjit Sharma bikramjit_...@yahoo.com wrote: On Tuesday, June 3, 2014 4:32 PM, Bikramjit Sharma bikramjit_...@yahoo.com wrote: Hi all, I tried to generate topology file for benzene (as a trial)  using topolbuild1_3. The itp file generated

[gmx-users] Simulation of wild and mutant types of HSA protein

Dear Gromacs users I have a question about protein simulation in Gromacs. We are interested in the effect of single point mutation on the structure of HSA (human serum albumin) protein. We selected a pdb file for wild type HSA and submitted it for MD simulation. One of the mutatns of HSA is

Re: [gmx-users] Prevent protein rotation - rectangular box

On 6/2/14, 9:43 PM, Steven Neumann wrote: Thanks but it will take some time to install 5.0 on the cluster. How about [ angle_restraints_z ]? I could think of an atom in the protein to restrain along z axis (protein length). Not sure how can I measure such an angle though and which atom to

Re: [gmx-users] rlist for implicit water

On 6/3/14, 4:15 AM, Urszula Uciechowska wrote: Dear Gromacs users, I would like to run simulations with implicit water. My protein system is quite big it contains 784AA. I prepared eM.mdp file (see below) however I am not sure if its ok especially the rlist what should I use there in case of

Re: [gmx-users] Confusion about itp file generated by topolbuild

On 6/3/14, 6:51 AM, Bikramjit Sharma wrote: Hi all, I tried to generate topology file for benzene (as a trial) using topolbuild1_3. The itp file generated is (ffben.itp in my case) #define _FF_GAFF #define _FF_AMBER #define _FF_USER [ defaults ] ;nbfunc comb-rule gen-pairs

Re: [gmx-users] Simulation of wild and mutant types of HSA protein

On 6/3/14, 8:19 AM, Negar Parvizi wrote: Dear Gromacs users I have a question about protein simulation in Gromacs. We are interested in the effect of single point mutation on the structure of HSA (human serum albumin) protein. We selected a pdb file for wild type HSA and submitted it for

Re: [gmx-users] Confusion about itp file generated by topolbuild

On Tue, Jun 3, 2014 at 2:35 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/3/14, 6:51 AM, Bikramjit Sharma wrote: Hi all, I tried to generate topology file for benzene (as a trial) using topolbuild1_3. The itp file generated is (ffben.itp in my case) #define _FF_GAFF #define _FF_AMBER

[gmx-users] isothermal-isometric ensemble on gromacs

Dear gromacs users, I’m trying to replicate the following paper http://www.ncbi.nlm.nih.gov/pubmed/?term=Desiccation+Induced+Structural+Alterations+in+a+66-Amino+Acid+Fragment+of+an+Anhydrobiotic+Nematode+Late+Embryogenesis+Abundant+(LEA)+Protein. According to the methodology, they used gromacs

[gmx-users] from coarse-grained to all atoms

Good afternoon, I have some trajectories of coarse-graned (CG) simulations obtained using the UNRES force field (not implemented in GROMACS). I'd like to apply the analysis protocol that I generally use for gromacs trajectories also to these one, but because there are no native tools, I was

Re: [gmx-users] isothermal-isometric ensemble on gromacs

On 6/3/14, 10:05 AM, Carlos Navarrro Retamal wrote: Dear gromacs users, I’m trying to replicate the following paper

Re: [gmx-users] rlist for implicit water

Dear Justin, How could I change the cut-offs to make the MD more faster in my case? /Urszula On 6/3/14, 4:15 AM, Urszula Uciechowska wrote: Dear Gromacs users, I would like to run simulations with implicit water. My protein system is quite big it contains 784AA. I prepared eM.mdp file

Re: [gmx-users] isothermal-isometric ensemble on gromacs

Well, the terminology is an old one, but not very common. An isometric ensemble is generally one in which the extension in the mechanical work term is kept constant. Thus, it may mean that the volume is kept constant in a volume/pressure system, that the area is kept constant in a area/surface

[gmx-users] Gromacs GPU no longer working together

Anyone know what might be the cause of this? Did I unwittingly update the nvidia drivers or something like that? Everything was working fine last week. This is what I see when I try to mdrun, even on .tpr files that worked before. 2 GPUs detected: #0: N/A, stat: insane #1: NVIDIA Quadro FX

[gmx-users] Out of disk space

Hello, I was running the final equilibration step (NTP) and i received an error saying that i was running out of disk space, the trajectory file writen has 2GB, and every retry will generate a file with the same size. I have looked for file size limit, but there is no limitation that i can find

Re: [gmx-users] rlist for implicit water

On 6/3/14, 12:21 PM, Urszula Uciechowska wrote: Dear Justin, How could I change the cut-offs to make the MD more faster in my case? Well, there are plenty of things one can do to improve performance, but the better question is whether or not one can maintain something physically sensible

Re: [gmx-users] New Molecule Topology

Hi, I tried ATB but it has wrong database files. For example, Gromacs united atom .itp file is missing Carbon 28,29 and 30. I hope I will get help from them on this matter. Thank you On Fri, May 30, 2014 at 2:06 AM, lloyd riggs lloyd.ri...@gmx.ch wrote: I think the Ausi ATB is a bit beter

Re: [gmx-users] Inserting aquaporin-1 in a bilayer with multiple lipids

The abstract from the linked paper describes the method pretty well. By applying a high lateral pressure, the protein is forced into the membrane. As for the other method that I had seen at a conference (which I meant to say in my previous message that I *couldn't* remember off the top of my

[gmx-users] Remove rotation around the center of mass

Dear gmx-users, I have some questions on the way that gromacs remove the rotation around the center of mass when set comm-mode = Angular” I have checked the related code for removing the rotation and have a question on how gromacs estimate the inertia tensor I. In gromacs, the inertia tensor

Re: [gmx-users] Prevent protein rotation - rectangular box

Thanks, unfortunately I have such restrictions. I have defined two atoms which I wish to be dummy in my system. I placed one in between 2 beta sheets on the one termini of my protein and copy it moving along the z axis to the other beta sheet. I found closest prtoein heavy atoms and made