[gmx-users] still don't know how to modify my input file: Re: energy minimization runs with error like too large force
hrhu75 at gmail.com
Mon Nov 22 16:15:34 CET 2004
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.
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
> > _______________________________________________
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> 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
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