Re: [gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD

Sure - I added the input files to the Redmine issue. Reza On May 14, 2013, at 9:21 AM, David van der Spoel wrote: > On 2013-05-13 21:57, Reza wrote: >> So I think I figured out what was causing the discrepancy of Charmm27 >> energies between gromacs and NAMD. It appears that it's related to th

Re: [gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD

On 2013-05-13 21:57, Reza wrote: So I think I figured out what was causing the discrepancy of Charmm27 energies between gromacs and NAMD. It appears that it's related to the gromacs version: energies from 4.5.7 and NAMD match very well while 4.6.1 gives energies that are different from both 4.

Re: [gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD

Here is the script: #!/bin/bash # note: you must have "par_all27_prot_lipid.prm" in the starting directory set -e PROGRAMS="/g1/home/resal/Programs" GMX_BIN_457="$PROGRAMS/gromacs/4.5.7/thread/bin" GMX_BIN_461="$PROGRAMS/gromacs/4.6.1/thread/bin" NMD_BIN="$PROGRAMS/namd/NAMD_2.9_Linux-x86_64-mu

Re: [gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD

So I think I figured out what was causing the discrepancy of Charmm27 energies between gromacs and NAMD. It appears that it's related to the gromacs version: energies from 4.5.7 and NAMD match very well while 4.6.1 gives energies that are different from both 4.5.7 and NAMD. Here are the results

Re: [gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD

Actually pdb which is similarly doesn't have velocity information. In this case however I'm mainly interested to see how the potential terms compare between the two packages with Charmm27 ff. Reza > > > On 5/3/13 11:33 AM, Reza wrote: >> Thanks Mark! >> >>> No, they weren't. See >>> http:

Re: [gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD

On 5/3/13 11:33 AM, Reza wrote: Thanks Mark! No, they weren't. See http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy You cannot hope to reproduce accurately the energy of a configuration if you let the coordinates be manipulated. The "rerun" option is interesting - in my ca

Re: [gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD

Thanks Mark! > No, they weren't. See > http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy > You cannot hope to reproduce accurately the energy of a configuration if > you let the coordinates be manipulated. > The "rerun" option is interesting - in my case however the potential ene

Re: [gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD

On Wed, May 1, 2013 at 2:32 PM, Reza Salari wrote: > Hi Justin, > > I actually did :) but it ended up being bigger than 50 kb so it needed > moderator approval to show up. I was hoping it would've been released by > now. I'll attach a the details below. > > Any help/hint is highly appreciated. >

Re: [gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD

Hi Justin, I actually did :) but it ended up being bigger than 50 kb so it needed moderator approval to show up. I was hoping it would've been released by now. I'll attach a the details below. Any help/hint is highly appreciated. Reza Details: *1)* Both systems were prepared using VMD "membran

Re: [gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD

On 4/30/13 4:19 PM, Reza Salari wrote: Hi I have set up two small systems, one with a single POPC lipid, and another system with 23 POPC's arranged as a lipid bilayer. I am hoping to do a similar comparison as in Table 1 in the Par Bjelkmar et al paper (porting charmm ff to gromacs) for my sys

[gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD

Hi I have set up two small systems, one with a single POPC lipid, and another system with 23 POPC's arranged as a lipid bilayer. I am hoping to do a similar comparison as in Table 1 in the Par Bjelkmar et al paper (porting charmm ff to gromacs) for my systems. My main question is that for the sing