[gmx-users] prodrg
Hector Martinez-Seara Monne
h.seara at qf.ub.es
Mon Oct 4 15:21:26 CEST 2004
David van der Spoel wrote:
>On Mon, 2004-10-04 at 08:13, Hector Mrz-Seara Monne wrote:
>
>
>>Thank you David for your help, I'm quite new in gromacs and many things
>>still lack on
>>my knowledge. Well I'm trying to reduce all the constants forces in the
>>*.itp file of my monomer.
>>By the way, the only constants that worry you where those of the
>>improper dihedral or also of the proper once
>>with the asterisk. And why PRODRG duplicate the colums of definitions
>>
>>(c0 c1 m) (c0 c1 m)
>>
>>, this is normal(this confuses me since the beginning)?
>>
>>
>This has to do with free energy calculations where you go from one
>definition to another. Does prodrg produce the m for impropers as well?
>
>
>
Hi david,
All contants forces definition provide from PRODRG, the number 1673 is
the given by the program
but for your coments is quite hight. Sorry, but for your answer I can't
know if you think I have also problems
with the proper dihedral also, Can you clarify this point please.
Thanks in advance for all your help.
Hector
>>Thanks.
>>
>>I've been looking for the configuration of my fonts and everything seems
>>to be allright. I'm using the netscape mail. I don't know
>>what is hapenning but I'll try to fix this problem in the near future
>>
>>spoel at xray.bmc.uu.se wrote:
>>
>>
>>
>>>>>Try equilibrating at lower temperature and/or with a shorter time step.
>>>>>In particular since you describe this resonance thing. Could it be that
>>>>>your force constants are too high? You should have roughly 20 time steps
>>>>>in a complete period of the fastest motion.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>Thanks in advance for all your help, it's been quite useful for me in
>>>>order to increase my knowledge on this suite.
>>>>I've been thinking in the last suggestion and I'm not sure about the
>>>>meaning. As I understand if I use high constants
>>>>for defining my proper dihedrals I have to reduce my time steep that
>>>>actually is quite small 1fs only or work at lower temperature.
>>>>Here the *.itp file of the monomer contain this lines that I have
>>>>specifically modify to have a planarity system.
>>>>
>>>>
>>>>
>>>>
>>>>
>>>First off, please turn off the weird fonts in your mail...
>>>
>>>In the improper definition below there are too many force constants,
>>>i.e. the thirs and sixth number (m) should go. Further the force
>>>constant is ten times higher than usual which means vibrations will be
>>>sqrt(10) times faster, which again means you will have to reduce the
>>>timestep. Reducing the force constant by a factor of ten will be fine
>>>too.
>>>
>>>
>>>
>>>
>>>>.....
>>>>[ dihedrals ]
>>>>;ai aj ak al fu c0 c1 m c0 c1 m
>>>> 9 12 10 8 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CBA CAD
>>>>CAE CAU
>>>> 14 15 13 11 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CBB NAV
>>>>CAF CAG
>>>> 17 16 20 18 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CBC NAW
>>>>CAH CAI
>>>> 22 23 21 19 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CBD OAY
>>>>CAJ CAK
>>>> 27 26 29 28 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CAZ CAT
>>>>OAX OAC
>>>> 17 18 19 22 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CBC CAI
>>>>CAK CBD
>>>> 18 19 22 21 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CAI CAK
>>>>CBD CAJ
>>>> 19 22 21 20 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CAK CBD
>>>>CAJ CAH
>>>> 22 21 20 17 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CBD CAJ
>>>>CAH CBC
>>>> 21 20 17 18 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CAJ CAH
>>>>CBC CAI
>>>> 20 17 18 19 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CAH CBC
>>>>CAI CAK
>>>> 9 10 11 14 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CBA CAE
>>>>CAG CBB
>>>> 10 11 14 13 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CAE CAG
>>>>CBB CAF
>>>> 11 14 13 12 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CAG CBB
>>>>CAF CAD
>>>> 14 13 12 9 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CBB CAF
>>>>CAD CBA
>>>> 14 15 17 16 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CBB NAV
>>>>CBC NAW
>>>> 13 12 9 10 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CAF CAD
>>>>CBA CAE
>>>> 12 9 10 11 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CAD CBA
>>>>CAE CAG
>>>> 4 3 2 1 1 0.0 5.9 3 0.0 5.9 3 ; DI
>>>>CAN CAM CAL CAA
>>>>.....
>>>> 11 14 15 16 1 180.0 53.5 2 180.0 33.5 2 ; DI CAG CBB
>>>>NAV NAW *
>>>> 15 16 17 20 1 180.0 53.5 2 180.0 33.5 2 ; DI NAV NAW
>>>>CBC CAH *
>>>>.....
>>>> 25 26 27 29 1 0.0 0.4 6 0.0 0.4 6 ; DI CAR
>>>>CAT CAZ OAX
>>>> 26 27 29 30 1 180.0 16.7 2 180.0 16.7 2 ; DI CAT CAZ
>>>>OAX HE2 *
>>>>
>>>>Do you know if your advise works equally for both proper and improper
>>>>dihedrals? If not can you tell me the diference?
>>>>I think for your coment that the dihedral with the asterisk that are
>>>>the problematic? witch time step will you use, or do you know any
>>>>way to avoid the restriction that my system contain?
>>>>
>>>>Thank you very much for taking your time to answer me, David. If you
>>>>think you need any other information or that is not clear what
>>>>I'm asking for just tell me and I can send you any indormation or
>>>>foles that you thing could be usefull to solve my actual problems
>>>>
>>>>
>>>>
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>>>>
>>>>
>>>>
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