Re: [gmx-users] LJ-SR and LJ-14

On 8/15/16 6:56 PM, Stella Nickerson wrote: If you want the "total" Lennard-Jones potential between two groups, would you simply add LJ-SR + LJ-14? If so, what is the utility of calculating both potentials separately? LJ-SR are normal nonbonded interactions within the short-range cutoff.

[gmx-users] LJ-SR and LJ-14

If you want the "total" Lennard-Jones potential between two groups, would you simply add LJ-SR + LJ-14? If so, what is the utility of calculating both potentials separately? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

Re: [gmx-users] Scc order parameter

There are some python codes to do that., Google it -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit

Re: [gmx-users] Loosing partly the available CPU time

Hi, Although I don't know what exactly is the system you are simulating, one thing is clear: you're pushing the parallelization limit with - 200 atoms/core - likely "concentrated" free energy interactions. The former that alone will make the run very sensitive to load imbalance and the latter

[gmx-users] Fwd: Restraints/constraints for keeping a helix as helical

Dear All, I was wondering if you have any comment or suggestion on this post. Any comment is appreciated in advance. Best, Mohsen -- Forwarded message -- From: Mohsen Ramezanpour Date: Wed, Aug 10, 2016 at 7:17 PM Subject: Restraints/constraints

Re: [gmx-users] Loosing partly the available CPU time

Hi Szilárd, Thanks for your response, please find below a link containing required files.log files. https://drive.google.com/file/d/0B_CbyhnbKqQDc2FaeWxITWxqdDg/view?usp=sharing Thanks, Cheers, Alex On Mon, Aug 15, 2016 at 2:52 PM, Szilárd Páll wrote: > Hi, > > Please

Re: [gmx-users] PDB file

On 8/15/16 9:30 AM, f.namazi...@sci.ui.ac.ir wrote: Hi Dear all; What are these columns "1.00" and "0.00" in PDB file? Google knows all about PDB format. -Justin for example: ATOM 10 N LEU A 2 4.595 6.365 3.756 1.00 0.00 N ATOM 11 CA LEU A 2

[gmx-users] (no subject)

*Hello,* *I **have recently tried to simulate a shear flow in a molecular dynamics model by implementing the **Lees Edwards boundary (periodic shear flow) conditions in GROMACS. However the * *results I got are strange ... * *I added the effect of the shear, delta_U(y)=gamma*dy, where gamma =

[gmx-users] PDB file

Hi Dear all; What are these columns "1.00" and "0.00" in PDB file? for example: ATOM 10 N LEU A 2 4.595 6.365 3.756 1.00 0.00 N ATOM 11 CA LEU A 2 4.471 5.443 2.633 1.00 0.00 C ATOM 12 C LEU A 2 5.841 5.176

Re: [gmx-users] Loosing partly the available CPU time

Hi, Please post full logs; what you cut out of the file will often miss information needed to diagnose your issues. At first sight it seems that you simply have an imbalanced system. Not sure about the source of the imbalance and without knowing more about your system/setup and how is it

Re: [gmx-users] genion

On 8/15/16 4:11 AM, f.namazi...@sci.ui.ac.ir wrote: Hi every body; Why we should neutralise net charge of the simulation system? To properly answer your question, we must approach it with a bit more nuance. One typically neutralizes the net charge of a condensed-phase system for two

[gmx-users] TPI and chemical potential

Dear list I am trying to teach myself how the test particle method for excess chemical potential calculations work. To this end, I created a small system of about 900 water molecules (TIP3p), and simulated for 1 ns. I then set up files for inserting an extra water molecule to calculate mu, the

Re: [gmx-users] genion

Depends on the simulation but in general, most of the biological systems occur at natural pH which around is 7.4, So mimicking the exact biological system we are neutralising the system. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] genion

Hi Farzaneh, If I am not entirely wrong; Otherwise, the tiny amount of charge in a single box would be huge in the calculation because of PBC(periodic boundary condition) and a coulomb explosion would happen. Cheers, Alex On Mon, Aug 15, 2016 at 10:11 AM, wrote: > Hi

[gmx-users] genion

Hi every body; Why we should neutralise net charge of the simulation system? Regards. Farzaneh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] _replay_Energy minimization, of peptide-ligand, tearing peptide apart

http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System Check Archive -- Regards, Nikhil Maroli -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read