[gmx-users] tip5p water model:Atomtype LP1 not found
jalemkul at vt.edu
Mon Apr 15 14:30:53 CEST 2013
On 4/15/13 8:28 AM, Ahmet yıldırım wrote:
> The norm of force is very high. And the system converged in 3 steps
> For example, I got the following results for spc water model
> Steepest Descents converged to Fmax < 1000 in 167 steps
> Potential Energy = -2.1208019e+05
> Maximum force = 9.8452704e+02 on atom 286
> Norm of force = 4.9830578e+01
Fnorm is not particularly high here or in the previous post. The fact that it
converged in 3 steps is also not unexpected. Minimizing a pure water system
that is built from pre-equilibrated blocks should be easy. The potential is
sensible and the maximum force is below your threshold. Everything is perfectly
> 2013/4/15 Justin Lemkul <jalemkul at vt.edu>
>> On 4/15/13 7:22 AM, Ahmet yıldırım wrote:
>>> I did as you said. I corrected number of water molecules in the topology
>>> grompp -v -f minim.mdp -c protein-water.gro -p topol.top -o
>>> Steepest Descents converged to Fmax < 1000 in 3 steps
>>> Potential Energy = -1.5700267e+05
>>> Maximum force = 7.2195142e+02 on atom 3761
>>> Norm of force = 1.3341200e+02
>>> I think these results isnt normal. isnt it?
>> What exactly do you think is wrong?
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> gmx-users mailing list gmx-users at gromacs.org
>> * Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>> * Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users