[gmx-users] PMF of ligand transport

Hi gromacs users, I am using Gromacs 4.0.4 package. I am doing SMD of a ligand transport through a channel. I performed SMD and did umbrella sampling (Thanks to Justin for his tutorial). Extracted frames with a window spacing interval of ~0.12nm. and did 1ns sampling. Histograms are with

Re: [gmx-users] PMF profile using g_wham with pull_geometry = distance for ion channel

Thomas Piggot wrote: Hi again, Just before I reside myself to rerunning a large number of simulations I was wondering if it is possible to just rerun the simulations where the ion is above and below the reference using pull_geometry=position. Then could I combine these with the other

Re: [gmx-users] PMF of ligand transport

Aswathy wrote: Hi gromacs users, I am using Gromacs 4.0.4 package. I am doing SMD of a ligand transport through a channel. I performed SMD and did umbrella sampling (Thanks to Justin for his tutorial). Extracted frames with a window spacing interval of ~0.12nm. and did 1ns sampling.

RE: [gmx-users] Lipid topologies, carving, etc

Alex, I used the membrane builder and even developed a script to convert that POPC into Gro53a6 - please contact me by personal email, if you want it. Afterwards I found, that the resulting protein/lipid system contained many overlaps between atoms and removing all the overlaps created a

Re: [gmx-users] PMF of ligand transport

Ok i will explain you in detail. Initially i pulled the ligand through the protein channel , using the given parameters. pull = umbrella pull_geometry= distance pull_dim = N N Y pull_start = yes pull_nstxout = 10

Re: [gmx-users] question about installing gromacs on a mac

On May 5, 2010, at 18:15 , Emily Curtis wrote: checking for mkl.h... yes checking for DftiComputeForward in -lmkl... no configure: error: Cannot find Intel Math Kernel Library = 6.0 I don't understand why it is not finding my Math Kernal Library. I also do not understand what

[gmx-users] distances between atoms in an electrostatic interaction

Dear Gromacs users, I have an electrostatic interaction in my structure between GLU and LYS. After minimization the distance between the Hydrogen molecule on the Lysine and the Oxygen on the GLU is reduced to 1.4 A°. Is it possible to pre-set this distance to be 1.6 A° instead? I realize

Re: [gmx-users] how to show structure results in Martini coarse-grained simulation?

xi zhao wrote: in fact, using Maritni coarse-grained force field in gromacs, corresponding top file is system top file,and gro file is only coordinates file for protein. I do not know what the file format for top2psf.pl in coarse-graind simulation! Within your system topology, you have

Re: [gmx-users] how to show structure results in Martini coarse-grained simulation?

xi zhao wrote: thank you for your suggestion! using 3ehz.itp as in input file, the script produced psf, but how to show structure corresponding for the particular time. I do not know using of NAMD or charmm file format ? Load a .pdb file into VMD, then load the .psf file as data into it.

Re: [gmx-users] distances between atoms in an electrostatic interaction

On 6/05/2010 8:00 PM, abdullah ahmed wrote: Dear Gromacs users, I have an electrostatic interaction in my structure between GLU and LYS. After minimization the distance between the Hydrogen molecule on the Lysine and the Oxygen on the GLU is reduced to 1.4 A°. *Is it possible to pre-set this

Re: [gmx-users] how to show structure results in Martini coarse-grained simulation?

xi zhao wrote: In fact, the structure show still unchange , I fell confused! What do you mean unchanged? Did you load your coarse-grained .pdb file, then the .psf file as data for it? The bonds should show up after you load the .psf file. There won't be any sort of animation, if

[gmx-users] luck message and running tests

I was able to make install. *After typing ./luck * I got the following message: I was detained, I was restrained *Is that bad? Also, I am trying to run the tests and I keep getting:* ERROR: Can not find grompp in your path. Please source GMXRC and try again. Does anyone know how to fix

Re: [gmx-users] luck message and running tests

Emily Curtis wrote: I was able to make install. *After typing ./luck * I got the following message: I was detained, I was restrained *Is that bad? Also, I am trying to run the tests and I keep getting:* That's the purpose of luck - spit out random funny quotes. ERROR: Can not find

[gmx-users] Extending MD run

Dear Gromacs users, I am using gromacs 3.3.3 for my simulation. I run my project for 5ns and want to extend to 10 ns. Can any body tell me if this is the right way to do. tpbconv -s previous.tpr -f previous.trr -e previous.edr -o next.tpr -extend timetoextend The previous.tpr means for

Re: [gmx-users] luck message and running tests

Justin, Thank you again! Your suggestion worked. Emily On Thu, May 6, 2010 at 11:55 AM, Justin A. Lemkul jalem...@vt.edu wrote: Emily Curtis wrote: I was able to make install. *After typing ./luck * I got the following message: I was detained, I was restrained *Is that bad? Also,

Re: [gmx-users] Lipid topologies, carving, etc

I see. Well, maybe doing the old school manual carving isn't a bad idea, after all. I still think your script is extremely useful, will definitely write to you if I need it. Thanks, Alex On Thu, May 6, 2010 at 1:44 AM, Kukol, Andreas a.ku...@herts.ac.uk wrote: Alex, I used the membrane

[gmx-users] Re: Extending MD run

tekle...@ualberta.ca wrote: Dear Gromacs users, I am using gromacs 3.3.3 for my simulation. I run my project for 5ns and want to extend to 10 ns. Can any body tell me if this is the right way to do. tpbconv -s previous.tpr -f previous.trr -e previous.edr -o next.tpr -extend timetoextend

Re: [gmx-users] Re: Density

Thank you Justine I have another question. I run my simulation for 5ns and when i just check the density of my solvent, the density did not look right. I used the N-H and P-R for the thermostat and barostat. Both shows the correct temperature and pressure (300K and 1bar). when I use the

Re: [gmx-users] Re: Density

tekle...@ualberta.ca wrote: Thank you Justine I have another question. I run my simulation for 5ns and when i just check the density of my solvent, the density did not look right. I used the N-H and P-R for the thermostat and barostat. Both shows the correct temperature and pressure (300K

[gmx-users] Topologies phosphoserine and phosphothreonine for ffamber99

Hi. I am trying tu run a protein under the ffamber99 force field. Has anyone used a topology of phosphoserine and phosphothreonine for this force field? Thanks, Esteban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the

Re: [gmx-users] Topologies phosphoserine and phosphothreonine for ffamber99

ithu wrote: Hi. I am trying tu run a protein under the ffamber99 force field. Has anyone used a topology of phosphoserine and phosphothreonine for this force field? Try here: http://www.pharmacy.manchester.ac.uk/bryce/amber#pro Although the topologies are in AMBER format, but with some