[gmx-users] LINCS warning involving hydrogen

[Daan van Aalten]

Hi Senthil

Do you also get this error with the unedited version of the
PRODRG-generated topology?
Is your starting structure reasonable - does it energy minimize well as
part of your total starting configuration?

cheers

Daan


On 29 Jul 2003, Senthil Kandasamy wrote:

> Hi all,
>
> I have a glycerol headgroup for a lipid and I am running into LINCS
> warnings during a short md run which eventually crashes.
>
> structure:
>
> H-O-CH2-CH-O-H
>          |
>          CH2-......lipid
>
> as united atoms:
>
> H-O-C-C-O-H
>       |
>       C-......lipid
>
> this is the warning I get :
> _____________________________________________
> Step 400, time 0.8 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 0.120018 (between atoms 334 and 335) rms 0.002054
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>     333    335   33.8    0.2081   0.2040      0.2000
>     334    335   72.2    0.1297   0.1120      0.1000
>    4311   4313   36.0    0.2086   0.1984      0.2000
>    4312   4313   78.1    0.1089   0.1081      0.1000
>    6147   6149   37.1    0.2184   0.1979      0.2000
>    6148   6149   75.7    0.1187   0.1077      0.1000
> ____________________________________________________
>
> 335, 4313 and 6149 are hydrogen atoms attached to the -CH-O- moiety.
> 333  4311 and 6147 are the carbon atoms of the -CH-O-H and
> 334  4312 and 6148 are the oxygen atoms of the -CH-O-H.
>
> What would prevent this hydrogen atom from moving around so much? How
> can I constrain it? Some earlier posts, mention something about the
> pairs directive. Should I remove all the pairs involving that hydrogen?
> I am a bit confused.
>
> (I had created the topology file using prodrg for this molecule and then
> edited it )
>
> Senthil
>
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>


##############################################################################

Dr. Daan van Aalten                    Wellcome Trust CDA Fellow
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk

        O     C           O     C         Visit the PRODRG server to take
        "     |           "     |         the stress out of your topologies!
  N--c--C--N--C--C--N--C--C--N--C--C--O
     |           "     |           "      http://davapc1.bioch.dundee.ac.uk/
     C-C-O       O   C-C-C         O             programs/prodrg/prodrg.html
       "
       O