[gmx-users] still don't know how to modify my input file: Re: energy minimization runs with error like too large force

[David van der Spoel]

On Mon, 2004-11-22 at 07:15 -0800, HR Hu wrote:
> Dear David:
>     Thanks for your kind reply so soon. But I still don't know how to
> modify the coordinates of the water 7773 generated by genbox.
> 
take it out and update your topology
>     Thank you very much!
> 
> 
> >   3. Re: energy minimization runs with error like too large    force
> >      on atom 7773 (David van der Spoel)
> > 
> > Message: 3
> > Date: Mon, 22 Nov 2004 09:21:32 +0100
> > From: David van der Spoel <spoel at xray.bmc.uu.se>
> > Subject: Re: [gmx-users] energy minimization runs with error like too
> >        large   force on atom 7773
> > To: HR Hu <hrhu75 at gmail.com>,   Discussion list for GROMACS users
> >        <gmx-users at gromacs.org>
> > Message-ID: <1101111692.17917.1.camel at vangogh>
> > Content-Type: text/plain
> > 
> > On Sun, 2004-11-21 at 17:32 -0800, HR Hu wrote:
> > > Hi, dear all,
> > >
> > > I am new in gromacs. Recently I perform a MD experiment with
> > > Gromacs3.2.1. I do agree that this software is so powerful.
> > > Here is my question: when I process to mdrun with em.mdp, the em.log
> > > output file shows the following information.
> > >
> > > "Stepsize too small, or no change in energy.
> > > Converged to machine precision,
> > > but not to the requested precision Fmax < 1000
> > >
> > > Double precision normally gives you higher accuracy.
> > > You might need to increase your constraint accuracy, or turn
> > > off constraints alltogether (set constraints = none in mdp file)
> > >
> > > Steepest Descents converged to machine precision in 960 steps,
> > > but did not reach the requested Fmax < 1000.
> > > Potential Energy = -4.9661972e+05
> > > Maximum force = 5.3885300e+05 on atom 7773
> > > Norm of force = 3.2573675e+06
> > >
> > > I try increase the stepsize "emstep" from 0.01 to 0.1, it still don't
> > > converge, the error remains. Then I check the atom 7773 and foud that
> > > it is an oxygen in a SOL water. Furthermore it is the bulk one, not
> > > the crystallographic one I keep in my system. As I know, the SPC216
> > > model is quite well optimized. Also I try to ignore this to process
> > > further position-restrained MD. It fails. I don't know why?
> > 
> > The energy is too low, you probably have a water molecule that has a
> > hydrogen too close to a negative charge in your protein.
> > 
> > >
> > > Second question is that how to discriminate the crystallographic water
> > > and the solvation ones generated by genbox? In original protein PDB
> > > files, the crystall ones are marked as HOH, but thereafter they are
> > > marked as same as the solvation water with SOL. I guess the atom
> > > sequense don't change before and after adding solvation water, am I
> > > right?
> > That's right. You will have your crystal waters first. They will
> > exchange quite soon though.
> > >
> > > My third, also the last one is that about my system contains protein,
> > > ligand and crystallographic water. If I attach the PRODRG converted
> > > ligand.pdb directly at the end of pdb/gro file(protein and HOH's atom
> > > No. or residue No. are continuous) generated by pdb2gmx. It will be
> > > error when process to genion. So I have to insert the ligand between
> > > the protein and HOH manuually to keep the No. of HOH and SOL
> > > continuous. Is there any other way to solve this negligible problem
> > > since it is too difficult for me to change the atom number and HOH
> > > numbere one by one if there are many crystallographic waters.
> > >
> > yes, write in your top at the end:
> > 
> > protein 1
> > sol X
> > ligand 1
> > sol Y
> > 
> > > Thanks in advance!
> > >
> > > Hairong Hu
> > > Ph.D.candidate
> > > Depart. of Chemistry
> > > Fudan University
> > > Shanghai, 200433,
> > > China
> > > hrhu75 at 163.com
> > > _______________________________________________
> > > 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.
> > --
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Assoc. 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
> _______________________________________________
> 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.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++