[gmx-users] Inconsistent shifts using multiple bonds type 6

TJ Piggot t.piggot at bristol.ac.uk
Tue Mar 6 01:22:00 CET 2007

Hi Mark thanks for your reply,

I'm not sure the problem is that these restraints are inappropriate, but 
the problem might be the sheer number. For example if i restrain a fairly 
large number of atom distances (say 100 Calpha distances) to the same 
length they are in the structure after minimisation and position restrained 
MD then mdrun still crashes, even if i use a very weak force for the 

I have also been playing round trying to fix the problem and have noticed 
from the mailing list that inconsistent shifts are seen when people are 
using infinite systems and have not set pbc=full. I know i am not using the 
kind of system but setting pbc=full does not result these problems that i 
see when i use pbc=xyz. Is pbc=full reasonable to use for production runs 
and does anyone know roughly how much slower it is (time is quite important 
as i have a large system)

Thanks again


--On 06 March 2007 09:57 +1100 Mark Abraham <mark.abraham at anu.edu.au> wrote:

>> Hello all,
>> I am trying to apply a set of harmonic distance restraints between pairs
>> of
>> protein atoms in my system, which is protein/ligand/water/ions in a
>> periodic box.
>> The way i am doing this is to use the bond type 6 and to add these bonds
>> at
>> the end of the [bonds] section in my topology file, after the system has
>> been energy minimised and i have performed position restrained MD,
>> without these harmonic distance restraints.
>> I can then run it through grompp with no problems and start mdrun. If i
>> only have a few (ie less than about 30) harmonic distance restraints then
>> the simulation if fine and runs happily. However if i increase the number
>> of restraints then mdrun crashes due to lincs warnings and it also says
>> that the are inconsistent shifts, (the number of inconsistent shifts
>> varies
>> depending on which atoms i choose to restrain and also the number of
>> atoms chosen) a warning not seen with less harmonic distance restraints.
> Why do you need more harmonic restraints?
>> I should also say that i have run this system without these harmonic
>> restraints without problems for tens of nanoseconds already. Also this
>> problem can be repeated if i try to use the [distance_restraints] however
>> it requires less restraints to get the inconsistent shift warning (and
>> lincs problems) this way.
>> If anyone can give me an idea of what is causing this problem it would be
>> warmly appreciated, or even just how to detect which of the harmonic
>> distance restraints will cause the problem before i run mdrun so i can
>> replace the problem 'bonds' in the topology file.
> You can't tell a priori, but if you watch the trajectory you should start
> to get an idea what is breaking where and this will narrow down the number
> of inappropriate restraints.
> Mark
> _______________________________________________
> 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.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.

More information about the gromacs.org_gmx-users mailing list