Re: [gmx-users] gmx check precision

On 3/30/18 7:29 AM, jt555 wrote: Hello there, I am currently using GROMACS version 5.1.2 and had a question in relation to the gmx check command. The following appears on the screen after invocation of gmx check -f protein.pdb: GROMACS: gmx check, VERSION 5.1.2 Executable:

[gmx-users] gmx check precision

Hello there, I am currently using GROMACS version 5.1.2 and had a question in relation to the gmx check command. The following appears on the screen after invocation of gmx check -f protein.pdb: GROMACS: gmx check, VERSION 5.1.2 Executable: /usr/bin/gmx Data prefix: /usr Command line:

Re: [gmx-users] gmx check

Thank you for explaining. Best wishes, Dawid 2017-07-28 15:11 GMT+02:00 Mark Abraham : > Hi, > > Seems like the extremes of normal variation of unconstrained bonds. As gmx > help check suggests, the feature exists as a quick sanity check. The use of > "correct" is in

Re: [gmx-users] gmx check

Hi, Seems like the extremes of normal variation of unconstrained bonds. As gmx help check suggests, the feature exists as a quick sanity check. The use of "correct" is in the sense of "between sensible atom indices" rather than suggesting that only one length is valid. Mark On Fri, 28 Jul 2017

Re: [gmx-users] gmx check

Hi, No, those bonds I get the message were not constrained and virtually in every frame there is different bunch of bonds for which I get this message. Because the whole output from gmx check is 1.1 GB, I just give you a few examples. Reading frame 0 time0.000 # Atoms 24884 Precision

Re: [gmx-users] gmx check

Hi, It's hard to tell without seeing the messages and knowing whether those bonds were constrained. Mark On Fri, 28 Jul 2017 13:19 Dawid das wrote: > Dear Gromacs Users, > > I get a bunch of communicates when I run > gmx check -f npt-md2.xtc -s1 npt-md2.tpr >&

[gmx-users] gmx check

Dear Gromacs Users, I get a bunch of communicates when I run gmx check -f npt-md2.xtc -s1 npt-md2.tpr >& gmx-check2.out saying that I get different bond lengths than they should be. Can that be caused by only 0.001 nm precision of my results? Also I am not exactly sure if I understand correctly