Thank you mark.
On Wed, Apr 11, 2012 at 6:15 AM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > On 11/04/2012 4:13 AM, ramesh cheerla 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 > > > Isn't that a totally different box? See editconf -h about -angles. > > Mark > > > 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.abra...@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 >> -- >> gmx-users mailing list gmx-users@gromacs.org >> 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 gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > > > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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