Re: [gmx-users] linc warnings

subarna thakur wrote: Hi, I am using the following keywords in pr.mdp file for the simulation for protein with fe4s4 cluster; title = Yo cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt

Re: [gmx-users] linc warnings

Justin A. Lemkul wrote: snip were harmonically restrained to their initial positions of pdb, How can I do this for my fe4s4 cluster. What keywords should I use for that and in which step I can do? That's what position restraints are doing. I should amend this slightly. I assumed your

[gmx-users] some molecule clashing with another ?

Hi My simulation broke down and the simulation procedues are as follows. 1. center a protein molecule in the simulation box 2. put 20 ligands around the protein with genbox command 3. make sure that any atom of the ligands does not overlap on any atom of the protein with Visulization-software.

Re: [gmx-users] some molecule clashing with another ?

Chih-Ying Lin wrote: Hi My simulation broke down and the simulation procedues are as follows. 1. center a protein molecule in the simulation box 2. put 20 ligands around the protein with genbox command 3. make sure that any atom of the ligands does not overlap on any atom of the

[gmx-users] some molecule clashing with another ?

Hi The follwing is my .out file. From it, can I conclude that some molecule clashing with another ? Thank you Lin Step -2, time -0.002 (ps) *LINCS WARNING* relative constraint deviation after LINCS: max 0.044043 (between atoms 366 and 368) rms 0.001724 bonds that rotated more than 30 degrees:

Re: [gmx-users] some molecule clashing with another ?

Chih-Ying Lin wrote: Hi The follwing is my .out file. From it, can I conclude that some molecule clashing with another ? No, you can conclude that your system is unstable. One possible reason is atomic clashing, but you cannot say for sure. General advice on your problem (which is

[gmx-users] How to modify or avoid some molecule clashing with another ?

Hi After reading the log file and watching the trajectory movies(nstxout = 1), some molecule clashes with another in my simulation system. How can i avoid the situation happening again? How to modify the broken simulation? Thank you Lin Message: 4 Date: Wed, 30 Dec 2009 19:00:51 -0500

Re: [gmx-users] How to modify or avoid some molecule clashing with another ?

Chih-Ying Lin wrote: Hi After reading the log file and watching the trajectory movies(nstxout = 1), some molecule clashes with another in my simulation system. How can i avoid the situation happening again? How to modify the broken simulation? Two options come to mind: 1.

[gmx-users] some molecule clashing with another ?

Hi I print out the energy EM-solvated.edr file here. Since the average is high, is it caused by the molecule clashing? I selected potential, kinetic, total energy. What else energy should I print out to learn the broken simulation system? Thank you Lin Select the terms you want from the

Re: [gmx-users] some molecule clashing with another ?

Chih-Ying Lin wrote: Hi I print out the energy EM-solvated.edr file here. Since the average is high, is it caused by the molecule clashing? It means there's something badly wrong. For the usual sort of biomolecular MD simulation, PE should be negative, around 10^-4 to 10^-6 kJ/mol

[gmx-users] LINCS WARNING max 597108032.000000 (between atoms 366 and 368) ?

Hi what does the max max 597108032.00 (between atoms 366 and 368) mean? is it the max force or max length of the system? where is the max force listed? max 597108032.00 (between atoms 366 and 368) rms 26394490.00 bonds that rotated more than 30 degrees: what does previous, current

Re: [gmx-users] LINCS WARNING max 597108032.000000 (between atoms 366 and 368) ?

Chih-Ying Lin wrote: Hi what does the max max 597108032.00 (between atoms 366 and 368) mean? is it the max force or max length of the system? where is the max force listed? Don't know. max 597108032.00 (between atoms 366 and 368) rms 26394490.00 bonds that rotated more than 30

Re: [gmx-users] LINCS WARNING max 597108032.000000 (between atoms 366 and 368) ?

Chih-Ying Lin wrote: Hi what does the max max 597108032.00 (between atoms 366 and 368) mean? is it the max force or max length of the system? where is the max force listed? It corresponds to the length between the constrained atoms. Forces are printed to the .trr file if you have

[gmx-users] clashing happened inside the protein molecule?

Hi Here is my .out file. atoms 366 and 368 are two atoms inside the protein. What is other possible way to solve it ? Thank you Lin relative constraint deviation after LINCS: max 597108032.00 (between atoms 366 and 368) rms 26394490.00 bonds that rotated more than 30 degrees: atom

[gmx-users] Break ? = Position restrained MD

Hi In the position restrain MD, only solvent molecules and hydrogen atoms are allowed to move. I checked the .out file. The max is happened on the atoms inside protein. Why? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] Break ? = Position restrained MD

Chih-Ying Lin wrote: Hi In the position restrain MD, only solvent molecules and hydrogen atoms are allowed to move... appreciably under normal conditions. However if you have a medium restraining force and a ridiculously large LJ force, guess who wins? I checked the .out file. The

[gmx-users] gromacs 4.06 binary for linux -redhat

Hi I am new to GROMACS, like to use it. I would be appreciate if anyone can direct me to the right place where I could get the linux binary either x32/x64 - redhat. I could not compile the source cause it is looking for FFTW etc.,. thanks venkat -- gmx-users mailing list

Re: [gmx-users] gromacs 4.06 binary for linux -redhat

venkat wrote: Hi I am new to GROMACS, like to use it. I would be appreciate if anyone can direct me to the right place where I could get the linux binary either x32/x64 - redhat. Binaries for newer versions probably haven't been made yet. Your subject line points to version 4.0.6,