On 1/10/10 5:18 PM, Jack Shultz wrote:
I am trying to get this workflow opperational. However, my systems are
getting unstable. I have preped two mdp files: 1) one for restrained 2)
unrestrained. LINCS errors appear for restrained and unrestrained has
infinite energy appearing.
http://boinc.drugdiscoveryathome.com/_em_restrained_rcs_mdrun.txt_
<http://boinc.drugdiscoveryathome.com/em_restrained_rcs_mdrun.txt>
__
This log file shows several "long bond" warnings, which may be the root of your
problem. See here:
http://www.gromacs.org/Documentation/Errors#Long_bonds_and.2for_missing_atoms
Since your minimization is failing immediately, there is something physically
unreasonable about your structure, such that EM cannot resolve the problem.
Note, too, that one of the long bond warnings pertained to atom 1668, which is
the location of the first LINCS warning. Coincidence? Not likely. Re-examine
the starting structure and figure out if anything is missing or poorly
reconstructed (e.g., from initially missing atoms).
This is where I get the LINCS Warnings
Step -1, time -0.001 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.461520, max 14.428611 (between atoms 1668 and 1669)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Steepest Descents:
Tolerance (Fmax) = 1.00000e+04
Number of steps = 100
Warning: 1-4 interaction between 1658 and 1672 at distance 2.655 which
is larger than the 1-4 table size 2.400 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
Step= 0, Dmax= 1.0e-02 nm, Epot= 1.09364e+09 Fmax= 2.21154e+11,
atom= 3292
Step 1, time 0.001 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.680509, max 22.293625 (between atoms 1668 and 1670)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
What is a reasonable increase in table-extension. Is this a mis-leading
suggestion?
You should not adjust the table-extension. The other part of the error message
is what you need to pay attention to ("your system is exploding").
-Justin
Here is the log from the unrestrained minimization.
http://boinc.drugdiscoveryathome.com/_em_rcs_mdrun.txt_
<http://boinc.drugdiscoveryathome.com/em_rcs_mdrun.txt>
Here is a zip archive containing the working directory for this
minimization. Its about 428 kb
http://boinc.drugdiscoveryathome.com/rcs_ga_run_10_bt_Fzd2-MD7-MD8-7.zip_lig_24205_ChemDiv_5754-2873_ts_1263004110202172000.zip
--
Jack
http://drugdiscoveryathome.com
http://hydrogenathome.org
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
