[gmx-users] Re: berger-oplsaa combination for DPC micelle

lwatersremoved.pdb -p berger_opls.top -po test_min1out.mdp -pp test_min1out.top -o min1.tpr Thank you in advance for your advice. I am completely stuck at this step. Cheers, Soo Mei Original Message Subject:Re: berger-oplsaa combination for DPC micelle Date: Thu, 05 Jun 2008 0

[gmx-users] Re: berger-oplsaa combination for DPC micelle

min1out.mdp -pp test_min1out.top -o min1.tpr Thank you in advance for your advice. I am completely stuck at this step. Cheers, Soo Mei Original Message Subject:Re: berger-oplsaa combination for DPC micelle Date: Thu, 05 Jun 2008 02:42:58 +0800 From: Low Soo Mei &l

[gmx-users] Re: berger-oplsaa combination for DPC micelle

Hi, Thank you Chris for the helpful answer! I have modified the atomtype names to follow dmpc.itp, which is more familiar to me, but those names are also the same as popc.itp. There is probably something wrong with the way I did it because although the "atomtype not found" errors have stopp

[gmx-users] berger-oplsaa combination for DPC micelle

Hi Gromacs users, I am trying to simulate a protein with a micelle, and have used dpc.itp from Dr. Tieleman's site. I have also introduced parts of lipid.itp into ffoplsaanb.itp and ffoplsaabon.itp in accordance with Chris Neale's half-epsilon double-pairlist method. But when I issue a gromp

[gmx-users] .trr file

Hi all, I am quite new to Gromacs and would like to ask why the full _restart_ file .trr is designed such that every frame's coordinates and velocities are retained? In NAMD and Amber only the last frame's coordinates and velocities are necessary for a restart. I mention this because am wo

[gmx-users] grompp -np -shuffle with position restraints

Hi Gromacs users, When I run grompp for 16 nodes to prepare my file for parallel run on my cluster, and also -shuffle to spread the load evenly over the nodes, I find that the position restraints get shuffled as well. This is my command line: grompp -v -f heat.mdp -c min_end.pdb -p dmpc_npa

[gmx-users] Re: combining differently-generated force-fields

A related reference might be this? Comparison of protein force fields for molecular dynamics simulations. Methods Mol Biol. 2008;443:63-88. Guvench O, Mackerell AD Jr. Not that I've read it yet, because my institute doesn't have access to that journal. Cheers, Soo Mei

[gmx-users] Re: upgrade version - "make distclean"?

Thanks David and Mark for your helpful comments. Just to follow up, make uninstall works very well - I executed it in the directory that was untarred from the source 3.3.2 tarball, and it removed all the 3.3.2 files in both that directory and the /usr/local/gromacs (default installation path).

[gmx-users] upgrade version - "make distclean"?

Hi, I would like to upgrade from version 3.3.2 to 3.3.3 on my local computer, non-parallel for both. Can I confirm that I should 1) cd to the gromacs-3.3.2 directory 2) type "make distclean" 3) then delete the entire gromacs-3.3.2 directory , to clean 3.3.2 off my computer entirely? I am s

[gmx-users] gmx_sumi src/mdlib/rf_util.c fix

Hi, Sorry to post again so soon and for a rather simple problem. I have a similar mdrun crash as Michel, here http://www.gromacs.org/pipermail/gmx-users/2007-November/030491.html but I could not understand David's solution... There was also no related email on the list more recent than Mich

[gmx-users] Re: syntax for switching between multiple position restraint .itp in the .top file

charset=ISO-8859-1; format=flowed Low Soo Mei wrote: Hi gmx-users, If I use different position restraints during each stage of minimization, should I separately write all my restraints in the same .top file in this manner, #ifdef LIPID_ALL_POSRE #include "lipid_all_posre.itp&quo

[gmx-users] syntax for switching between multiple position restraint .itp in the .top file

_posre.itp" #elseif WATER_POSRE #include "water_posre.itp" #else #include "lipid_headgroup_posre.itp" Thanks for your help in advance. Cheers, Soo Mei -- Ms. Low Soo Mei Research Assistant Biomolecular Modelling and Design G