[gmx-users] virtual sites

site to a carbohydrate along with the peptides? -- Regards, Dr. Neha S. Gandhi, Curtin Research Fellow, School of Biomedical Sciences, Curtin University, Perth GPO U1987 Australia LinkedIn Research Gate -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx

[gmx-users] virtual sites in gromacs

75 0.988 4.044 3.539 -- Regards, Dr. Neha S. Gandhi, Curtin Research Fellow, School of Biomedical Sciences, Curtin University, Perth GPO U1987 Australia LinkedIn Research Gate -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please

[gmx-users] xpm2ps

and maximum tick spacing however I always get black lines at the bottom instead of X-axis. Your input is appreciated. -- Regards, Dr. Neha S. Gandhi, Curtin Research Fellow, School of Biomedical Sciences, Curtin University, Perth GPO U1987 Australia LinkedIn Research Gate -- gmx-users mailing listgmx

[gmx-users] Axis of the box in Gromacs

Hi everybody, I was wondering if you could answer a quick question I had. Where does the axis in a box with PBC lie in Gromacs? I thought 0, 0, 0 was the corner of the box, but if that was true none of the x, y, z values for position should be negative. However in my trajectory I see a value with

[gmx-users] RE: Is non-linear data output/storage possible?

Justin Lemkul wrote The .cpt file stores information related to output frequency. The existing.cpt file designates output every X steps, while the new .tpr file specifies output every Y steps, and X != Y, so mdrun complains. I'm assuming mdrun aborts at that point? Have you tried with

[gmx-users] RE: Is non-linear data output/storage possible?

Hi everybody, I started changing init-step. Now I seem to have another problem. When I go to switch to another 'block' it tells me that my input and checkpoint states are not identical when I use mdrun the second time. I am not sure how they can be any different as I only have one .cpt file in

[gmx-users] RE: Is non-linear data output/storage possible?

The .cpt file stores information related to output frequency. The existing .cpt file designates output every X steps, while the new .tpr file specifies output every Y steps, and X != Y, so mdrun complains. I'm assuming mdrun aborts at that point? Have you tried with -noappend? Hi, So

[gmx-users] Squishing or Stretching Membranes

Hello everybody, I had a question about trjconv. After one of my simulations has ended I want to use the final structure file to run some other simulations. However, what I want to do is run an NVT run using the average box size of the earlier run. Since the final structure file will most likely

[gmx-users] RE: Is non-linear data output/storage possible?

-bounces@ [mailto:gmx-users- bounces@ ] On Behalf Of Neha Sent: Thursday, 6 June 2013 11:00 PM To: gmx-users@ Subject: [gmx-users] Is non-linear data output/storage possible? Hi everybody! This is a sort-of general question that I am not sure where to find the answer for. I am

[gmx-users] RE: Is non-linear data output/storage possible?

Hi, So the commands are: grompp -f 10step.mdp -p dppc_bilayer.top -o 10step.tpr -c dppc_bilayer.gro mdrun -nt 4 -s 10step.tpr -c nonlinear.gro -e nonlinear.edr -x nonlinear.xtc -o nonlinear.trr -g nonlinear.log -cpo nonlinear.cpt -rdd 2.5 grompp -f 100step.mdp -c 10step.tpr -p

[gmx-users] RE: Is non-linear data output/storage possible?

Lemkul wrote On Tue, Jul 2, 2013 at 1:23 PM, Neha lt; nshafique@ gt; wrote: Hi, So the commands are: grompp -f 10step.mdp -p dppc_bilayer.top -o 10step.tpr -c dppc_bilayer.gro mdrun -nt 4 -s 10step.tpr -c nonlinear.gro -e nonlinear.edr -x nonlinear.xtc -o nonlinear.trr -g

[gmx-users] Extending Simulations

Hi everybody, I have a question that relates to reproducibility in Gromacs. If I have a .cpt file from a previous simulation and use that for two simulations using tpbconv, how similar should the temperature graphs etc be? When I use the .edr files to plot various properties, there is significant

[gmx-users] Re: Membrane Runs Crashing

Hi everybody, My runs keep crashing despite energy minimisation and fiddling around with nstlist values. I have been looking in the Gromacs manual particularly the interaction ranges in the domain decomposition section, which mentions that simulations can stop with error messages about missing

[gmx-users] Re: Membrane Runs Crashing

Justin Lemkul wrote What was the outcome of EM before this? What if you try NVT before NPT? Have you tried reducing the timestep or the value of nstlist? I would try everything with ref_p = 1.0 instead of zero to make sure you can get a normal setup to work. -Justin The membrane

[gmx-users] Re: Membrane Runs Crashing

Here's the full mdp file. Please let me know if you need anymore information and thank you so much for helping! ; RUN CONTROL PARAMETERS = integrator = md ; start time and timestep in ps = tinit= 0.0 dt = 0.02 nsteps =

[gmx-users] Membrane Runs Crashing

Hi everybody! I am trying to simulate a lipid membrane at zero pressure and at a range of temperatures. I am using a bilayer from the Martini website. I was having a problem with the Parinello-Rahman barostat so I switched to Berendsen and am also keeping the height of the box constant otherwise

[gmx-users] Re: Membrane Equilibration

Hi everybody, It seems that my runs still are crashing. I even decided not to switch over to Parinello-Rahman and continue doing the simulation with a Berendsen barostat and it shuts off after a period of time. I am extremely puzzled as to why this is happening especially since Berendsen is

[gmx-users] Re: Membrane Runs Crashing

Hi, Well, I tried running a simulation at ref_p to 1.0 and got the same error as earlier, so it doesn't seem to be that. That was the only thing I changed in the mdp file, so I am still not sure as to where the problem is. Justin Lemkul wrote On 6/18/13 3:13 PM, Neha wrote: Hi everybody! I

[gmx-users] Membrane Equilibration

Hi everybody, I am trying to simulate a lipid bilayer and wanted to use Parrinello Rahman coupling. However, I read that Parinello-Rahman is not great for equilibration so I thought I would do a small run using the Berendsen barostat to decrease the chances of large oscillations. I then used the

[gmx-users] Re: Membrane Equilibration

is an okay way to do what I want? Again thanks for the help! Justin Lemkul wrote On 6/11/13 1:13 PM, HANNIBAL LECTER wrote: ref_p= 0.0 0.0 ?? Are you sure about this?? That's a likely culprit. See below for another. On Tue, Jun 11, 2013 at 5:22 PM, Neha lt; nshafique

[gmx-users] Re: Membrane Equilibration

Hi, I am using the Martini field for those who wanted to know. My values for the mdp file for ref_p were inspired from this paper as it says pressure was coupled anisotropically to 0 bar in all directions. http://www.sciencedirect.com/science/article/pii/S0005273611002045 I think I will try

[gmx-users] Seeing Martini membrane trajectory files

Hi everybody! I have a quick question about VMD and trajectory files. It seems that VMD should be able to be use to view Gromacs trajectory files. I am working with lipid membranes, and I was able to view the final .gro file with VMD. However I was not able to see the entire trajectory, and I am

[gmx-users] Is non-linear data output/storage possible?

Hi everybody! This is a sort-of general question that I am not sure where to find the answer for. I am running a simulation on the order of tens of microseconds. However I also want to do some analysis on the order of very small time steps but I do not want to save the data of very small time

[gmx-users] Getting .edr file data as a generic data file

in the .edr files in a more pliable format. Please let me know if you know how to do this! I am a completely new user to Gromacs and appreciate all the help possible. -Neha -- View this message in context: http://gromacs.5086.x6.nabble.com/Getting-edr-file-data-as-a-generic-data-file-tp5008863.html Sent

[gmx-users] Creating a monolayer from Martini bilayer

Hello everybody, I am a new user to Gromacs and am working on lipid simulations with the Martini forcefield. The Martini website provides a pre-equilibrated DPPC bilayer, and I was wondering if there were any told that would allow me to convert this bilayer into a monolayer. For periodic boundary

[gmx-users] Re: Creating a monolayer from Martini bilayer

Hi, thank you so much! This way seems promising, however I am not sure how to center the bilayer around z=0. I thought I could use editconf but I might be confused as to how Gromacs centers its objects. If I put -center 0 0 0 does that mean the bilayer is centered around z = 0? Also I thought

[gmx-users] Re: Creating a monolayer from Martini bilayer

a lot of elaboration! Tsjerk Wassenaar wrote Hi Neha, A single structure is like a trajectory with only one frame :p trjconv works on those as well. Right, set the center at 0,0,0 and choose the lipids as group for centering. Cheers, Tsjerk On Mon, Jun 3, 2013 at 7:31 PM, Neha lt

[gmx-users] xpm2ps issue

10009. Upon do_dssp analyses only on 300 frames, ticks on both Y and X-axis are visible. How can one play around with scales on X-axis? I tried tweaking -bx and -size parameters but didn't help. Any feedback is appreciated. -- Regards, Dr. Neha S. Gandhi, Curtin Research Fellow, School

[gmx-users] Query on generate velocities and gen_temp in mdp files for REMD simulations

. Replica exchange -What should be gen_temp and gen_velocity set to? Many thanks, Neha -- Regards, Dr. Neha S. Gandhi, Curtin Research Fellow, School of Biomedical Sciences, Curtin University, Perth GPO U1987 Australia LinkedIn Research Gate -- gmx-users mailing listgmx-users@gromacs.org

RE: [gmx-users] error with indexfile

First check your .gro file and your .top file, to make sure atom 6518 (or Water) is consistently defined. Next step would be to make sure this atom features in the index file within a correct group. In some cases, if a single atom is left out and not part of any group in the index file, it gives

[gmx-users] Constraints for md simulations of carbohydrates

Dear List, I want to study the ring puckering of carbohydrates. Is it recommended to use hydrogen-bond constraints or i simply put none in constraints section in the md.mdp file? Many thanks, Regards, Neha Gandhi Gajaria, School of Biomedical Sciences, Curtin University of Technology, GPO Box

[gmx-users] topolbuild

Hi List, I have downloaded topolbuild1.2.1 but cannot extract files. Can anyone help and check the link? Many thanks -- Regards, Neha Gandhi Gajaria, School of Biomedical Sciences, Curtin University of Technology, GPO Box U1987 Perth, Western Australia 6845 -- gmx-users mailing listgmx

[gmx-users] Simulation at unrealistic temperatures

is very much appreciated. Regards, Neha Gandhi Gajaria, School of Biomedical Sciences, Curtin University of Technology, GPO Box U1987 Perth, Western Australia 6845 aneal.mdp Description: Binary data md.mdp Description: Binary data -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] GROMOS carbohydrate forcefield 45a4

parameters are important to validate ff for such molecules? Your help is appreciated. -- Regards, Neha Gandhi, School of Biomedical Sciences, Curtin University of Technology, GPO Box U1987 Perth, Western Australia 6845 ___ gmx-users mailing listgmx-users

[gmx-users] drug-enzyme simulation.

that 5ns gives issues. 2) I ran another similar but smaller system and the complex is stable even after 8ns. What went wrong with the simulations in case 1? Is there a way to fix this problem? Your help is much appreciated. Regards, Neha Gandhi, School of Biomedical Sciences, Curtin University

Re: [gmx-users] drug-enzyme simulation.

Many thanks Justin, It worked! 2009/3/29 Justin A. Lemkul jalem...@vt.edu: Neha Gandhi wrote: Hi List, 1) I m running a drug -enzyme simulation. I ran 62 ps of simulated annealing followed by  production runs of 5ns usng NPT and PBC and PME.. After 5ns, the protein moves far away from

[gmx-users] Drug-Enzyme tutorial- LIE energies in gromacs

is preferred for polar solutes (drugs) like sugars. What is the reference for these values for polar solutes i.e. sugars.? I would appreciate if there is any example of such calculation done in gromacs. Many thanks, Regards, Neha Gandhi, School of Biomedical Sciences, Curtin University of Technology, GPO

[gmx-users] Re: Drug-Enzyme tutorial- LIE energies in gromacs

was wondering if there are reports where LIE has been parameterise using PME and PBC. Thanks and Regards, Neha 2009/3/24 Neha Gandhi n.gandh...@gmail.com Dear GMX-users, In the Gromacs Drug/Enzyme complex solvation tutorial by John E. Kerrigan , in the end they mention about the LIE calculation