[gmx-users] question

[Mark Abraham]

On Sun, Dec 31, 2017, 06:14 RAHUL SURESH <drrahulsuresh at gmail.com> wrote:

> On Sat, 30 Dec 2017 at 9:47 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 12/30/17 1:39 AM, s.ghasemlou wrote:
> > > Hello every one,
> > >
> > > After using the command "g_grompp -f em.mdp -c totalbox1.gro -p
> > > topol.top -o ions.tpr" I get the error:
> > >
> > > ERROR 1 [file topol.top, line 863]:
> > >    ERROR: The cut-off length is longer than half the shortest box
> vector
> > > or
> > >    longer than the smallest box diagonal element. Increase the box size
> > > or
> > >    decrease rlist.(my box vectors are 31.16343- 31.16343- 31.16343)
> >
> > Check to be sure; it seems impossible to me that conventional cutoffs
> > could trigger such an error with such a large box. Make sure that you're
> > not thinking in A and trying to use nm (GROMACS convention).
> >
> > > I have tried different rlist, r columb and rvdw values. I have also
> > > changed the box vector several times, but I still get the same error. I
> > > don't know how to change them to fix the error.
> > >
> > > There is also the below warning:
> > >
> > > Warning: atom name 1 in topol.top and totalbox1.gro does not match (H55
> > > - OW)
> > > Warning: atom name 2 in topol.top and totalbox1.gro does not match (C2
> -
> > > HW1)
> > > Warning: atom name 3 in topol.top and totalbox1.gro does not match (H53
> > > - HW2)
> > > Warning: atom name 4 in topol.top and totalbox1.gro does not match (H54
> > > - OW)
> > > Warning: atom name 5 in topol.top and totalbox1.gro does not match (C1
> -
> > > HW1)
> > > Warning: atom name 6 in topol.top and totalbox1.gro does not match (H51
> > > - HW2)
> > > Warning: atom name 7 in topol.top and totalbox1.gro does not match (H52
> > > - OW)
> > > Warning: atom name 8 in topol.top and totalbox1.gro does not match (C50
> > > - HW1)
> > > Warning: atom name 9 in topol.top and totalbox1.gro does not match
> (H109
> > > - HW2)
> > > Warning: atom name 10 in topol.top and totalbox1.gro does not match
> > > (H110 - OW)
> > > Warning: atom name 11 in topol.top and totalbox1.gro does not match
> (O43
> > > - HW1)
> > > Warning: atom name 12 in topol.top and totalbox1.gro does not match
> (C42
> > > - HW2)
> > > Warning: atom name 13 in topol.top and totalbox1.gro does not match
> (C44
> > > - OW)
> > > Warning: atom name 14 in topol.top and totalbox1.gro does not match
> (C40
> > > - HW1)
> > > Warning: atom name 15 in topol.top and totalbox1.gro does not match
> (C41
> > > - HW2)
> > > Warning: atom name 16 in topol.top and totalbox1.gro does not match
> > > (H100 - OW)
> > > Warning: atom name 17 in topol.top and totalbox1.gro does not match
> (C46
> > > - HW1)
> > > Warning: atom name 18 in topol.top and totalbox1.gro does not match
> > > (H102 - HW2)
> > > Warning: atom name 19 in topol.top and totalbox1.gro does not match
> (C45
> > > - OW)
> > > Warning: atom name 20 in topol.top and totalbox1.gro does not match
> > > (H101 - HW1)
> >
> > Your topology is out of order with respect to the coordinates. The order
> > of the [molecules] section in your .top must be identical to the order
> > of the appearance of coordinates. This is not the case in your system,
> > so you need to correct it. Do not use -maxwarn under any circumstances;
>
>
> Dear Justin
>
> 1. For The above mentioned error is it advisable to manually edit the gro
> file or top file?
>

Once you've decided what you want to simulate, all the input files must be
consistent with that. Change any that aren't.

2. What will the situation to use the flag “-maxwarn” ?
>

If you understand what is causing the situation and why it is not a
problem. That does not apply in your case.

Mark


> > you will get a physically invalid system.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Virginia Tech Department of Biochemistry
> >
> > 303 Engel Hall
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalemkul at vt.edu | (540) 231-3129
> > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> >
> > ==================================================
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.