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 <[email protected]>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 <[email protected]> > 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 <[email protected]> > > 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 > >> -- > >> gmx-users mailing list [email protected] > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at > >> 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 [email protected]. > >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > -- > > gmx-users mailing list [email protected] > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > > 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 [email protected]. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > -- > 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 > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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