Re: [gmx-users] Umbrella sampling

Hi, I try to use umbrella sampling for calculating PMF. i change distance between protein and ZNS nanosheet. I use gomacsV4.5.4 after minimization and equilibration. i use: grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -o pull.tpr this is md_pull.mdp: integrator =

[gmx-users] Topology for Charmm, regarding

Dear all I have generated a structure.par file using ffTK toolkit of VMD. To use it in gromacs I have generated the structure.top file using topoltool plugin of vmd. 1. Now, how can i generate "itp" file to carry out, protein-ligand simulation? 2. Will it be sufficient if I generate "gro" file

Re: [gmx-users] How to run MD with longer recording interval to reduce the file size?

Hello, Thank you Justin and Qinghua! Can I ask 1) I could not find "nstfout" (forces) in the md.mdp file from the tutorial. Should I add a new line of "nstfout=0"? Yeah, you can add that line, or you can leave it be, the default is set as ZERO. 2) should I change "nstxout-compressed=5000" to

Re: [gmx-users] How to run MD with longer recording interval to reduce the file size?

Thank you Justin and Qinghua! Can I ask 1) I could not find "nstfout" (forces) in the md.mdp file from the tutorial. Should I add a new line of "nstfout=0"? 2) should I change "nstxout-compressed=5000" to "nstxout-compressed=5"? 3) Do you mean using "compressed-x-grps=Protein" will set

Re: [gmx-users] The sum of the two largest charge group radii (X) is larger than rlist

The sum of the two largest charge group radii (7.984601) is larger than rlist (0.347900). the configuration looks fine across pbc. Everything looks normal. Following is my md. I have user-specified potential so I need to have cut-off values as given below. integrator= md dt

Re: [gmx-users] How to run MD with longer recording interval to reduce the file size?

Hello, Here is the settings I used in the mdp file, you may consider it. nstxout = 0 ; save coordinates every 2 ps nstvout = 0 ; save velocities every 2 ps nstxtcout   = 500   ; xtc compressed trajectory output every 2 ps nstenergy   =

Re: [gmx-users] The sum of the two largest charge group radii (X) is larger than rlist

On 12/15/17 4:26 AM, Faezeh Pousaneh wrote: Hi, I get this error only in NVT equlibration step, not in the NPT and production steps. Should I worry about it? In gromacs page it tell the error can come from 4 reasons, but how I can recognize which can be mine? Check the size of your largest

Re: [gmx-users] determining the unbinding path

On 12/15/17 5:30 AM, abhisek Mondal wrote: Hi, For performing Umbrella Sampling Simulation of protein ligand system how should one device the proper unbinding path, as in case of biological systems unbinding paths can be various ? Few words regarding this issue would be highly

Re: [gmx-users] Can't read xxx bytes of pullf.xvg to compute checksum

On 12/15/17 5:44 AM, Diez Fernandez, Amanda wrote: Dear users, I am running many (almost identical) simulations and every so often one crashes and I get this message. Initially I just deleted everything, started from scratch and the problem was solved. However it is starting to be annoying.

Re: [gmx-users] How to run MD with longer recording interval to reduce the file size?

On 12/15/17 7:34 AM, ZHANG Cheng wrote: Dear Qinghua, Thank you very much. Do you mean set "nstvout" and "nstenergy" as 0? nstenergy is the frequency of writing energy terms to the .edr file. It has no effect on the .trr, which is only impacted by nstxout (coordinates), nstvout

Re: [gmx-users] How to run MD with longer recording interval to reduce the file size?

Dear Qinghua, Thank you very much. Do you mean set "nstvout" and "nstenergy" as 0? Also, how to set xtc-grps as a group? The original md.mdp file is: title = OPLS MD simulation ; Run parameters integrator = md; leap-frog integrator nsteps = 1

Re: [gmx-users] How to run MD with longer recording interval to reduce the file size?

Hello, Normally, you don't need to write out the force and velocity, then you can set nstfout and nstvout as ZERO, then only the coordinates will be written out in a xtc file. If you don't care about waters, then you can also set xtc-grps as a group without waters and counterions. Best,

[gmx-users] Can't read xxx bytes of pullf.xvg to compute checksum

Dear users, I am running many (almost identical) simulations and every so often one crashes and I get this message. Initially I just deleted everything, started from scratch and the problem was solved. However it is starting to be annoying. Any idea what is happening? Is it an error of

[gmx-users] How to run MD with longer recording interval to reduce the file size?

Dear Gromacs, I am following Justin's tutorial of "Lysozyme in Water" to run the MD. The .trr file got more than 10 GB after 30 ns. So I plan to run a MD with less frequent intervals. In the md.mdp file, the "dt = 0.002". My understanding is to change the five "5000" into "5" to achieve

[gmx-users] determining the unbinding path

Hi, For performing Umbrella Sampling Simulation of protein ligand system how should one device the proper unbinding path, as in case of biological systems unbinding paths can be various ? Few words regarding this issue would be highly appreciated. Please suggest few references

[gmx-users] The sum of the two largest charge group radii (X) is larger than rlist

Hi, I get this error only in NVT equlibration step, not in the NPT and production steps. Should I worry about it? In gromacs page it tell the error can come from 4 reasons, but how I can recognize which can be mine?