[gmx-users] Place water away from existing atoms
s.neumann08 at gmail.com
Thu May 17 17:50:31 CEST 2012
My tube is finite. I increased my box so the water could interact with all
water molecules. The same problem: My minim.mdp
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 10.0 ;
emstep = 0.001
nsteps = 50000 ; Maximum number of (minimization) steps to perform
nstxout = 1
; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long
ns_type = grid ; Method to determine neighbor list (simple, grid)
rlist = 1.4 ; Cut-off for making neighbor list (short range
coulombtype = PME ; Treatment of long range electrostatic
rcoulomb = 1.4 ; Short-range electrostatic cut-off
rvdw = 1.4 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)
Well... no clue...
On Thu, May 17, 2012 at 4:16 PM, Steven Neumann <s.neumann08 at gmail.com>wrote:
> Thank you. Is it possible that this is caused by the trapped molecules
> inside my tube? My tube ends are on the box edges so water cannot migrate
> outside the tube where are the other water molecules.
> On Thu, May 17, 2012 at 3:59 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>> On 5/17/12 10:38 AM, Steven Neumann wrote:
>>> Well, I am still getting the same error when I try to do minimization:
>>> molecule on atom X cannot be settled" - these water molecules are not
>>> close to
>>> the Tube surface. If I will remove them the same error will occur but on
>>> other atoms. If I specified only vdwradii for my Tube atoms why in the
>>> bulk of
>>> water there are some overlaps? Can you please help?
>> The problem is not necessarily with the water molecule, but is more often
>> indicative of some other instability in the system, such that forces are
>> transmitted to that poor unsuspecting water molecule and it blows up.
>> It's hard to diagnose, so make sure you're EM step is very small and you
>> save configurations frequently in order to diagnose what's happening. It
>> could be a problem with the .mdp file, topology, or perhaps some weird
>> water overlap, but if that's the case, then genbox didn't do it, something
>> else caused it.
>> 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>
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users