[gmx-users] Box generation for monoclinic crystal - regd

ramesh cheerla rameshgromacs at gmail.com
Tue Apr 10 22:17:03 CEST 2012 

Dear Tsjerk,

Thank you for your reply, I will try to work with PDB format and get back
to you.

On Wed, Apr 11, 2012 at 12:22 AM, Tsjerk Wassenaar <tsjerkw at gmail.com>wrote:

> Hi Ramesh,
>
> Maybe it is easier, and less error-prone, to work in PDB format,
> specifying the box as a CRYST1 record. You can use the PDB format
> anywhere in your workflow where GRO format is used.
>
> Cheers,
>
> Tsjerk
>
>
> On Tue, Apr 10, 2012 at 8:13 PM, ramesh cheerla <rameshgromacs at gmail.com>
> wrote:
> > Dear Mark,
> >
> >              Thank you for reply, sorry for not being very clear, Here
> my
> > doubt is can i use  triclinic box for the simulations of the crystal
> whose
> > unit cell is monoclinic. As i said earlier  i have tried editconf as
> > editconf -f input.gro -o out_box1.gro  -bt triclinic -box 3.22 2.608
> 7.792
> >  -angles 90  125.4 90
> > it gave the following warning
> >
> > WARNING: Triclinic box is too skewed.
> >
> > for clarity here i am sending a part of the output file generated by the
> > editconf
> > God Rules Over Mankind, Animals, Cosmos and Such
> >  6528
> >     1PEGA    C1    1  -0.025   0.408  -0.045
> >     1PEGA    C2    2  -0.015   0.326   0.084
> >      ::::::::::::::::::::::::::::::::::::::::::::::::::::::::;
> >      3.22000   2.60800   6.35148   0.00000   0.00000   0.00000   0.00000
> > -4.51376  -0.00000
> > if i change the angles while using the editconf i observed the following
> > changes
> >
> > editconf -f input.gro -o out_box2.gro  -bt triclinic -box 3.22 2.608
> 7.792
> >  -angles 90  90 125.4
> > in this case editconf haven't given any warning and the output as follows
> >
> >  God Rules Over Mankind, Animals, Cosmos and Such
> >  6528
> >     1PEGA    C1    1   1.477   0.167   0.675
> >     1PEGA    C2    2   1.487   0.085   0.804
> >      ::::::::::::::::::::::::::::::::::::::::::::::::::::::::;
> >    3.22000   2.12585   7.79200   0.00000   0.00000  -1.51077   0.00000
> > -0.00000  -0.00000
> >
> > Can you please help me in this regard.
> >
> > thank you in advance.
> >
> >
> >
> >
> >
> >
> >
> >
> > On Mon, Ap;r 9, 2012 at 11:55 AM, Mark Abraham <Mark.Abraham at anu.edu.au>
> > wrote:
> >>
> >> On 9/04/2012 3:22 PM, ramesh cheerla wrote:
> >>>
> >>> Dear Gromacs users,
> >>>
> >>>                           I am planing to simulate a polymeric crystal
> in
> >>> gromacs, which is of monoclinic unit cell with cell parameters a =
> 0.805 nm
> >>> b = 1.304 nm and c = 1.948 nm and beta = 125.4 deg. my crystal is of
> 424
> >>> type  i.e 4 unit cells along 'a' direction  '2' unit cells along 'b'
> >>> direction and 4 unit cells along 'c' direction.
> >>> So my box vector lengths are a = 3.22 nm, b = 2.608 nm, c = 7.792 nm.
> >>> I  am using editconf to generate box for this crystal as:
> >>>
> >>> editconf -f input.gro -o out_box.gro  -bt tric -box 3.22 2.608 7.792
> >>>  -angles 90  125.4 90
> >>>
> >>> Here i have some doubts:
> >>>
> >>> 1) Am i using the editconf in correct manner for generation of box for
> >>> the monoclinic crystal, though the crystal is of monoclinic  i am
> using box
> >>> type as triclinic
> >>> i haven't found any specific method for the generation of box for the
> >>> monoclinic crystal.
> >>> 2) Is there any specific method to generate the box for the monoclinic
> >>> crystals.
> >>> 3) The notations for the lattice parameters of the crystal i.e 'a' ,
> 'b'
> >>> , 'c' and angles alpha, beta , gamma used by crystallography and the
> gromacs
> >>> editconf are the same or different, why because if i use editconf as
> above i
> >>> am getting the following warning:
> >>>
> >>> WARNING: Triclinic box is too skewed.
> >>
> >>
> >> This means equation 3.3 of the manual is not true. Maybe beta should be
> >> acute? I've no idea of necessity or convention here.
> >>
> >> Inspecting the whole output of editconf is probably instructive, but
> >> you've kept all that information to yourself instead of re-thinking how
> your
> >> repeat post might be constructed so as to make it easier / more likely
> for
> >> people help you. Likewise the final line of out_box.gro. Make sure you
> have
> >> read and understood what documentation is available with editconf -h
> and in
> >> manual section 3.2.
> >>
> >> Mark
> >> --
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> >
> >
> >
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
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