[gmx-users] Difference in alpha and thole terms for drudeFF

Justin, Hope this finds you well. Im curious if you could provide some insight regarding the differences i’m seeing in the alpha and thole values when comparing the GROMACS port of the drudeFF to the charmm version. I don’t see a common ratio coming out when comparing them and wasn’t sure

Re: [gmx-users] System almost blowing up

> > > On 4/4/17 9:31 AM, Dayhoff, Guy wrote: >>> >>> On 4/3/17 2:33 PM, Dayhoff, Guy wrote: >>>> >>>>>> Hi, >>>>>> >>>>>> I?m receiving a couple (~15) EM did not converge warnings as well as a &g

Re: [gmx-users] System almost blowing up

> > On 4/3/17 2:33 PM, Dayhoff, Guy wrote: >> >>>> Hi, >>>> >>>> I?m receiving a couple (~15) EM did not converge warnings as well as a >>>> few (~3) 1,4 interaction >>>> warnings during my run. It looks like it

[gmx-users] continuation with different dt values

Hi, I’m continuing a run and setting init-step as the total steps completed in the run i’m continuing from, if I change the dt for the continuation do I need to scale the steps previously taken? i.e going from dt = 1 to dt =2, completing 100 steps in the first sim, does init-step take the val

Re: [gmx-users] System almost blowing up

>> Hi, >> >> I?m receiving a couple (~15) EM did not converge warnings as well as a few >> (~3) 1,4 interaction >> warnings during my run. It looks like it starts down the path to blowing up >> but recovers. Is this ?recovery? >> system dependent? Should I take these messages (even without th

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 156, Issue 13

> Such a short dt and strict niter should not be necessary in practice. The > failure of SCF to converge/LINCS warnings is what we typically refer to as > polarization catastrophe, so your system is on the brink of instability. > This > is one of the inherent problems of SCF in polarizable s

[gmx-users] System almost blowing up

Hi, I’m receiving a couple (~15) EM did not converge warnings as well as a few (~3) 1,4 interaction warnings during my run. It looks like it starts down the path to blowing up but recovers. Is this “recovery” system dependent? Should I take these messages (even without the subsequent crash)

Re: [gmx-users] Drude-2013 FF, hardwall constraint errors with swm4-ndp water

> Your approach to "fix" the Drude coordinates is inappropriate. You're > negating > (1) the purpose of equilibration by resetting the coordinates and (2) the > polarizable model entirely. > - Got it, thanks. > The coordinate file provided on our website is already equilibrated and runs >

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 154, Issue 114

> Your approach to "fix" the Drude coordinates is inappropriate. You're > negating > (1) the purpose of equilibration by resetting the coordinates and (2) the > polarizable model entirely. Got it. > > The coordinate file provided on our website is already equilibrated and runs > indefinit

[gmx-users] EM did not converge crashing drude system

I have a drude system that I have minimized, and equilibrated through nvt and npt ensembles using position restraints (all with scf). As I perform the production runs i’m facing random crashes that seem to be related to EM did not converge messages. This has happened anywhere from tens of thousand

[gmx-users] gmx density scripting?

Is there a simple way to script the gmx density tool as to circumvent the need to manually select the groups from within the program? i.e. is there a way to specify the groups during the command call such as: gmx density -f traj.xtc -s input.tpr -ng 2 -grps 5,8 where -grps lets me tell it what g

Re: [gmx-users] topology

On Feb 27, 2017, at 6:00 AM, gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote: I am explaining my issues regarding complex simulation. I have 200ns conformer(OPLS FF) I have generated my ligand gro and itp file.(Using topolgen1_

[gmx-users] Drude-2013 FF, hardwall constraint errors with swm4-ndp wate

Hi, I'm experiencing an issue with the hardwall constraint used with the Drude FF during NVT runs employing Lagrangian dynamics which I have yet to rectify on my own. In short I'm using the GROMACS dev release obtained via: git clone git://git.gromacs.org/gromacs.git cd gromacs git che

[gmx-users] Drude-2013 FF, seg fault 11 on repeat minimization of beta-D-glucose monomer

Hi, Thanks for taking the time to humor my inquiry. I’m hoping to find a fix for my issue or obtain a working beta-D-glucose monomer model that I can use to continue troubleshooting my issue. Details below… (This is my first post, forgive me for including too much/ too little