[gmx-users] the target temperature
David
spoel at xray.bmc.uu.se
Tue Apr 6 22:33:01 CEST 2004
On Tue, 2004-04-06 at 22:21, Qi Sun wrote:
> Hi all the Gromacs users:
> I am a beginning of Gromacs and did some research on YASP before. My
> system is about pure Cyclohexane right now. total 674 molecules. There
> are two problems:
> 1. gen_vel is set to yes, and gen_temp is set to 325K. after I start
> even 1 number of step at dt (0.00000002). The temperature still starts
> from 4000~8000K high. I don't know what is going on.
> 2. Attached is my topology file, can somebody have a look and see if the
> topology file is wrong.
topology looks OK. How about the coordinates?
>
> Thank you so much.
>
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> Qi Sun
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> ______________________________________________________________________
> ;Topology for 674 Cyclohexane
> ;The force field files to be included
> #include "ffgmx.itp"
>
> [atomtypes]
> MEC 12.0 0.000 A 0.148927E-02 0.1854459E-05
> MEH 1.007825 0.000 A 0.222967E-03 0.6575946E-07
>
> [constrainttypes]
> MEC MEC 1 0.15
> MEC MEH 1 0.10
>
> [angletypes]
> ; i j k func th0 cth
> MEC MEC MEC 1 109.5 335
> MEC MEC MEH 1 109.5 420
> MEH MEC MEH 1 109.5 290
>
> [dihedraltypes]
> ; j k func phi0 cp mult
> MEC MEC 1 180.0 10 3
> ;This is Cyclohexane
> [moleculetype]
> Cyclohexane 3
>
> [atoms]
> ; nr type resnr residu atom cgnr charge
> 1 MEC 1 Cyclohexane C1 1 0
> 2 MEC 1 Cyclohexane C2 1 0
> 3 MEC 1 Cyclohexane C3 1 0
> 4 MEC 1 Cyclohexane C4 1 0
> 5 MEC 1 Cyclohexane C5 1 0
> 6 MEC 1 Cyclohexane C6 1 0
> 7 MEH 1 Cyclohexane H7 2 0
> 8 MEH 1 Cyclohexane H8 2 0
> 9 MEH 1 Cyclohexane H9 2 0
> 10 MEH 1 Cyclohexane H10 2 0
> 11 MEH 1 Cyclohexane H11 2 0
> 12 MEH 1 Cyclohexane H12 2 0
> 13 MEH 1 Cyclohexane H13 2 0
> 14 MEH 1 Cyclohexane H14 2 0
> 15 MEH 1 Cyclohexane H15 2 0
> 16 MEH 1 Cyclohexane H16 2 0
> 17 MEH 1 Cyclohexane H17 2 0
> 18 MEH 1 Cyclohexane H18 2 0
>
> [constraints]
> ; ai aj function constraint distance
> 1 2 1
> 2 3 1
> 4 3 1
> 5 4 1
> 5 6 1
> 1 6 1
> 1 7 1
> 1 8 1
> 2 9 1
> 2 10 1
> 3 11 1
> 3 12 1
> 4 13 1
> 4 14 1
> 5 15 1
> 5 16 1
> 6 17 1
> 6 18 1
>
> [pairs]
> ; ai aj funct c6 c12
> 1 4 1 0.0 0.0
> 1 11 1 0.0 0.0
> 1 12 1 0.0 0.0
> 1 15 1 0.0 0.0
> 1 16 1 0.0 0.0
> 2 5 1 0.0 0.0
> 2 13 1 0.0 0.0
> 2 14 1 0.0 0.0
> 2 17 1 0.0 0.0
> 2 18 1 0.0 0.0
> 3 6 1 0.0 0.0
> 3 7 1 0.0 0.0
> 3 8 1 0.0 0.0
> 3 15 1 0.0 0.0
> 3 16 1 0.0 0.0
> 4 9 1 0.0 0.0
> 4 10 1 0.0 0.0
> 4 17 1 0.0 0.0
> 4 18 1 0.0 0.0
> 5 7 1 0.0 0.0
> 5 8 1 0.0 0.0
> 5 11 1 0.0 0.0
> 5 12 1 0.0 0.0
> 6 9 1 0.0 0.0
> 6 10 1 0.0 0.0
> 6 13 1 0.0 0.0
> 6 14 1 0.0 0.0
> 7 9 1 0.0 0.0
> 7 10 1 0.0 0.0
> 7 17 1 0.0 0.0
> 7 18 1 0.0 0.0
> 8 9 1 0.0 0.0
> 8 10 1 0.0 0.0
> 8 17 1 0.0 0.0
> 8 18 1 0.0 0.0
> 9 11 1 0.0 0.0
> 9 12 1 0.0 0.0
> 10 11 1 0.0 0.0
> 10 12 1 0.0 0.0
> 11 13 1 0.0 0.0
> 11 14 1 0.0 0.0
> 12 13 1 0.0 0.0
> 12 14 1 0.0 0.0
> 13 15 1 0.0 0.0
> 13 16 1 0.0 0.0
> 14 15 1 0.0 0.0
> 14 16 1 0.0 0.0
> 15 17 1 0.0 0.0
> 15 18 1 0.0 0.0
> 16 17 1 0.0 0.0
> 16 18 1 0.0 0.0
>
> [angles]
> ; ai aj ak funct c0 c1
> 1 2 3 1
> 1 2 9 1
> 1 2 10 1
> 2 3 4 1
> 2 3 11 1
> 2 3 12 1
> 9 2 3 1
> 10 2 3 1
> 9 2 10 1
> 3 4 5 1
> 3 4 13 1
> 3 4 14 1
> 11 3 4 1
> 12 3 4 1
> 11 3 12 1
> 4 5 6 1
> 4 5 15 1
> 4 5 16 1
> 13 4 5 1
> 14 4 5 1
> 13 4 14 1
> 5 6 1 1
> 5 6 17 1
> 5 6 18 1
> 15 5 6 1
> 16 5 6 1
> 15 5 16 1
> 6 1 2 1
> 6 1 7 1
> 6 1 8 1
> 17 6 1 1
> 18 6 1 1
> 17 6 18 1
> 7 1 2 1
> 8 1 2 1
> 7 1 8 1
> [dihedrals]
> ; ai aj funct
> 1 2 3 4 1
> 2 3 4 5 1
> 3 4 5 6 1
> 4 5 6 1 1
> 5 6 1 2 1
> 6 1 2 3 1
> [system]
> ; Name
> Pure Cyclohexane
> [molecules]
> ; Compound #mols
> Cyclohexane 674
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. 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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