[gmx-users] LINCS error with 3.3
spoel at xray.bmc.uu.se
Wed Oct 12 18:02:09 CEST 2005
On Wed, 2005-10-12 at 23:20 +0800, Yang Ye wrote:
> I have re-runed grompp with old topology.
OK, please try this.
run grompp with 3.2.1 and with 3.3 and then run gmxcheck -s1 321.tpr -s3
330.tpr >& dump
(you'll need gmxcheck from 3.3). Look for suspicious differences.
Please do also run with the mdrun from 3.3 and the tpr file from 3.2.1
Then please report back to the mailing list and/or open a bugzilla.
Thanks for helping us debug gromacs 3.3.
> David van der Spoel wrote:
> >On Wed, 2005-10-12 at 18:11 +0800, Yang Ye wrote:
> >>Hi, Eric
> >>We tried to use release-3.3 to continue the running our existing
> >>simulations, on two platforms (x86_64 and alpha), with two systems (one
> >>big and one small ~20000 atoms). But we got lots of LINCS warning for
> >>both of them within 30 steps of the simulation, e.g.
> >>Step 22, time 0.044 (ps) LINCS WARNING
> >>relative constraint deviation after LINCS:
> >>max inf (between atoms 74 and 75) rms inf
> >>bonds that rotated more than 30 degrees:
> >> atom 1 atom 2 angle previous, current, constraint length
> >> 71 72 90.0 0.1090 0.8407 0.1090
> >> 74 75 90.0 0.1090
> >>311257572943502531345973775419542153121393363270638764032.0000 0.1090
> >> 93 94 90.0 0.1090 inf 0.1090
> >> 93 95 90.0 0.1090 inf 0.1090
> >>release-3.3 also generate lots of LINCS warnings with newly started system.
> >>Please advice whether you need more information to diagnose this?
> >Yes we need quite a bit more information. Did you rerun grompp with old
> >topologies, did you use an old tpr file, or did you make a new tpr with
> >tpbconv, if so which version?
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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