[gmx-users] Strange dgdl-value together with lincs
Maik Goette
mgoette at mpi-bpc.mpg.de
Fri Feb 15 09:27:24 CET 2008
Berk,
here comes the topology for this run (vdw morph):
Its OPLSAA and the hydrogens have bond terms. This is the standard
OPLSAA FF for ethane and methanol.
Thanks.
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
1 opls_135 1 E2M CB 1 0.0 12.011
opls_157 0.0 12.011
2 opls_140 1 E2M HB1 1 0.0 1.008
opls_156 0.0 1.008
3 opls_140 1 E2M HB2 1 0.0 1.008
opls_156 0.0 1.008
4 opls_140 1 E2M HB3 1 0.0 1.008
opls_156 0.0 1.008
5 opls_135 1 E2M CA 2 0.0 12.011
opls_154 0.0 15.9994
6 opls_140 1 E2M HA1 2 0.0 1.008
opls_155 0.0 1.008
7 opls_140 1 E2M HA2 2 0.0 1.008
DUM 0.0 1.008
8 opls_140 1 E2M HA3 2 0.0 1.008
DUM 0.0 1.008
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1 0.10900 284512.0 0.10900 284512.0
1 3 1 0.10900 284512.0 0.10900 284512.0
1 4 1 0.10900 284512.0 0.10900 284512.0
1 5 1 0.15290 224262.4 0.14100 267776.0
5 6 1 0.10900 284512.0 0.09450 462750.4
5 7 1 0.10900 284512.0 0.10900 284512.0
5 8 1 0.10900 284512.0 0.10900 284512.0
[ pairs ]
; ai aj funct c0 c1 c2 c3
2 6 1
2 7 1
2 8 1
3 6 1
3 7 1
3 8 1
4 6 1
4 7 1
4 8 1
[ angles ]
; ai aj ak funct c0 c1 c2
c3
2 1 3 1 107.800 276.144 107.800 276.144
2 1 4 1 107.800 276.144 107.800 276.144
2 1 5 1 110.700 313.800 109.500 292.880
3 1 4 1 107.800 276.144 107.800 276.144
3 1 5 1 110.700 313.800 109.500 292.880
4 1 5 1 110.700 313.800 109.500 292.880
1 5 6 1 110.700 313.800 108.500 460.240
1 5 7 1 110.700 313.800 110.700 313.800
1 5 8 1 110.700 313.800 110.700 313.800
6 5 7 1 107.800 276.144 107.800 276.144
6 5 8 1 107.800 276.144 107.800 276.144
7 5 8 1 107.800 276.144 107.800 276.144
[ dihedrals ]
; ai aj ak al funct c0 c1 c2
c3 c4 c5
2 1 5 6 3 0.62760 1.88280 0.00000
-2.51040 0.00000 0.00000 0.94140 2.82420 0.00000
-3.76560 0.00000 0.00000
2 1 5 7 3 0.62760 1.88280 0.00000
-2.51040 0.00000 0.00000 0.62760 1.88280 0.00000
-2.51040 0.00000 0.00000
2 1 5 8 3 0.62760 1.88280 0.00000
-2.51040 0.00000 0.00000 0.62760 1.88280 0.00000
-2.51040 0.00000 0.00000
3 1 5 6 3 0.62760 1.88280 0.00000
-2.51040 0.00000 0.00000 0.94140 2.82420 0.00000
-3.76560 0.00000 0.00000
3 1 5 7 3 0.62760 1.88280 0.00000
-2.51040 0.00000 0.00000 0.62760 1.88280 0.00000
-2.51040 0.00000 0.00000
3 1 5 8 3 0.62760 1.88280 0.00000
-2.51040 0.00000 0.00000 0.62760 1.88280 0.00000
-2.51040 0.00000 0.00000
4 1 5 6 3 0.62760 1.88280 0.00000
-2.51040 0.00000 0.00000 0.94140 2.82420 0.00000
-3.76560 0.00000 0.00000
4 1 5 7 3 0.62760 1.88280 0.00000
-2.51040 0.00000 0.00000 0.62760 1.88280 0.00000
-2.51040 0.00000 0.00000
4 1 5 8 3 0.62760 1.88280 0.00000
-2.51040 0.00000 0.00000 0.62760 1.88280 0.00000
-2.51040 0.00000 0.00000
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
Berk Hess wrote:
>
> I assume your are using a united atom model.
> What are the bonded parameters for the methanol H
> in the ethane topology?
> Does it have the normal methanol bond and angle potential?
> If these parameters are zero, I would indeed expect a spike.
>
> Berk.
>
>> Date: Thu, 14 Feb 2008 18:10:59 +0100
>> From: mgoette at mpi-bpc.mpg.de
>> To: gmx-users at gromacs.org
>> Subject: [gmx-users] Strange dgdl-value together with lincs
>>
>> Hi
>>
>> While trying to find, whats wrong with some of my free energy
>> calculation, I stumbled upon a strange thing, I don't understand.
>>
>> I'm simulating the interconversion of ethane to methanol in vacuum.
>> I'm splitting the process into 3 steps:
>> 1. charge of perturbed atoms -> 0
>> 2. morph of LJ-parameters and bonds
>> 3. charge of perturbed atoms -> B-state values
>>
>> Each system is morphed with 1 fs timestep and within 50 steps.
>> The total energies at the "borders" of the simulations (qqoff/vdw,
>> vdw/qqon, qqon/vdw and vdw/qqoff) perfectly match and show no jump; the
>> following simulation always got energies and velocities from the one before.
>>
>> Now, when running the LJ morph A->B with lincs, the dgdl looks like this:
>> http://www.mpibpc.mpg.de/groups/grubmueller/start/people/mgoette/images/dgdl_lincs_01.png
>> For B->A:
>> http://www.mpibpc.mpg.de/groups/grubmueller/start/people/mgoette/images/dgdl_lincs_10.png
>> Doing both without lincs yields:
>> http://www.mpibpc.mpg.de/groups/grubmueller/start/people/mgoette/images/dgdl_nolincs_01.png
>> For B->A
>> http://www.mpibpc.mpg.de/groups/grubmueller/start/people/mgoette/images/dgdl_nolincs_10.png
>>
>> I find this spike in the first step extremely strange. Additionally it
>> only occurs, when using shake or lincs as constraint solver. I guess, in
>> a longer process it will contribute to the integral in a neglectable
>> manner, but maybe theres some bug. The latest CVS shows the same behaviour.
>>
>> Any comments on that?
>>
>> Regards
>>
>> --
>> Maik Goette, Dipl. Biol.
>> Max Planck Institute for Biophysical Chemistry
>> Theoretical & computational biophysics department
>> Am Fassberg 11
>> 37077 Goettingen
>> Germany
>> Tel. : ++49 551 201 2310
>> Fax : ++49 551 201 2302
>> Email : mgoette[at]mpi-bpc.mpg.de
>> mgoette2[at]gwdg.de
>> WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
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>
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