Re: [gmx-users] mdrun error

pragya chohan wrote: Hi justin I placed POPC membrane in a box too of same dimension as the box of alamethicin and centred it too so that alamethicin is placed correctly in the membrane. I am attaching the pdb please have a look. Any help would be appreciated Check out http://wiki.gromacs.or

RE: [gmx-users] mdrun error

Pragya, I just realized that I may have read your message incorrectly. If you'd like to send me your PDB file off-list, I'd be happy to have a look. -Justin Quoting "Justin A. Lemkul" <[EMAIL PROTECTED]>: > Quoting pragya chohan <[EMAIL PROTECTED]>: > > > Hi justin > > I placed POPC membrane i

RE: [gmx-users] mdrun error

Quoting pragya chohan <[EMAIL PROTECTED]>: > Hi justin > I placed POPC membrane in a box too of same dimension as the box of > alamethicin and centred it too so that alamethicin is placed correctly in the > membrane. > I am attaching the pdb please have a look.Any help would be appreciated Looks

RE: [gmx-users] mdrun error

Hi justin I placed POPC membrane in a box too of same dimension as the box of alamethicin and centred it too so that alamethicin is placed correctly in the membrane. I am attaching the pdb please have a look.Any help would be appreciated Pragya > Date: Sat, 10 Nov 2007 12:42:01 -0500> From:

Re: [gmx-users] trjorder does not write trajectory file

It works fine for me under 3.3.1 - what command line are you issuing? -Justin Quoting Dmytro Kovalskyy <[EMAIL PROTECTED]>: > > Trjorder does not write trajectory file, only nshell.xvg > > This is true for 3.3.2 and 3.3.1 versions. > > Dima > > > ___

[gmx-users] trjorder does not write trajectory file

Trjorder does not write trajectory file, only nshell.xvg This is true for 3.3.2 and 3.3.1 versions. Dima ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gr

[gmx-users] Ace-Ala-Nac to Ace-Gly-Nac

Dear Bharat, OK, I went ahead and ran with your topologies using my own run scripts. My runs haven't finished yet, but looking at just values from equilibration, I seem to be seeing roughly the same trends you do. In particular: (1) The forward simulation always gives dv/dlambda values that are

Re: [gmx-users] soft-core and coulomb transformation

Bharat, Your values for the first set of calculations (the forward case?) below look really weird. I suspect you have something messed up in those runs. Have you checked that your define statements worked properly, and checked your run input files? In particular, your is staying almost constant a

RE: [gmx-users] mdrun error

Quoting pragya chohan <[EMAIL PROTECTED]>: > Thanks Justin for your reply. I am generating the starting structure through > genbox. > I added popc as solvent around alamethicin after aligning alamethicin in a > box and centering it in the box and followed same procedure for popc also. Do > you hav

RE: [gmx-users] mdrun error

Thanks Justin for your reply. I am generating the starting structure through genbox. I added popc as solvent around alamethicin after aligning alamethicin in a box and centering it in the box and followed same procedure for popc also. Do you have any better way? > Date: Sat, 10 Nov 2007 10:22

RE: [gmx-users] mdrun error

Since alamethicin works on its own, it suggests to me that the introduction of alamethicin into POPC is what's causing the problem, and judging by the enormous potential energies and forces, it appears to be bad contacts/atomic overlap (at least, that's been the cause of problems in my experience).

RE: [gmx-users] mdrun error

> Date: Fri, 9 Nov 2007 09:01:48 -0500> From: [EMAIL PROTECTED]> To: gmx-users@gromacs.org> Subject: Re: [gmx-users] mdrun error>> Check out the wiki at:>> http://wiki.gromacs.org/index.php/Errors#LINCS_warnings>> Alternatively, search the list for some

Re: [gmx-users] grompp doesn't process topology file of a DNA fragment using ffamber ports for gromacs

Mark Abraham wrote: I installed ffamber ports for gromacs, generated gro and topology files for a DNA structure with pdb2gmx, a box with editconf and added solvation with genbox. When I try to run grompp i obtain these errors: checking input for internal consistency... calling cpp -traditional.