[gmx-users] genion II
Pedro Alexandre de Araujo Gomes Lapido Loureiro
paloureiro at biof.ufrj.br
Fri Mar 8 19:31:14 CET 2002
I managed to get an answer to part of my questions in the e-mail by hugo:
">>You are probably using conjugate gradients with single precision mdrun.
>>This can be problematic for algorithmic reasons. If you are just preparing
>>for a MD run, conjugate gradients is overkill, and you can use steep.
>>Conjugate gradients minimizes better, but you typically need this only
>>when preparing for normal mode analysis, in which case you need doube
But if I run a MD after some steepest descent, there is a halt in the program
due to deviation in LINCS.
For those who are following this discussion, my previous e-mail was:
""""after using the program genion, to insert a Cl ion a box containing a
in water I got the following warnings/errors:
1)After runnig the program grompp (mshion.top and mshion1-1.gro already contain
"Warning: atom names in mshion.top and mshion1-1.gro don't match (Cl - OW)
(more than 20 non-matching atom names)
Warning 7 [file "mshion.top", line 33]:
33145 non-matching atom names
atom names from mshion.top will be used
atom names from mshion1-1.gro will be ingnored"
In the .top file I had already added one Cl atom and deleted one water
Am I doing somethig wrong?
2)When using the random insertion mode in the genion, later when I run a
conjugate gradient minimization (after having runned a steepest descent without
Tolerance = 1.00000e+02
Starting Energy = 1.639584000000000e+09
F-Norm = 6.35435e+07
Step 1, E-Pot = 1.6376719360e+09, F-max = 5.34807e+10
Fatal error: ci = -2147483648 should be in 0 .. 2495 [FILE nsgrid.c, LINE 214]"
What does it mean ?
There was an e-mail with this kind of error in the list, but I was not able to
find any reply.
3)Using the electrostatic insertion mode gives the same error, when I use mdrun
to run a conjugate gradient minimization """"
Pedro Alexandre Lapido Loureiro
Laboratório de Física Biológica
Instituto de Biofísica
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