Re: [gmx-users] Programs to add residues

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<http://www.gromacs.org/Support/Mailing_Lists> > -- Michael Lerner, Ph.D. IRTA Postd

[gmx-users] Re: Temperature decreasing with NVE MARTINI lipid simulation

-grained molecular models” by M. Winger, D. Trzesniak, R. Baron and W. F. van Gunsteren, Phys. Chem. Chem. Phys., 2009, 11, 1934,” Physical Chemistry Chemical Physics 12, no. 9 (2010): 2254. On Tue, Jun 15, 2010 at 10:44 PM, Michael Lerner wrote: > Hi, > > I want to run some MAR

[gmx-users] Temperature decreasing with NVE MARTINI lipid simulation

txout = 10 annealing = no constraint_algorithm = Lincs pbc = xyz rcoulomb = 1.2 compressibility = 5e-5 5e-5 energygrps = Prot SOL ns_type = grid nstfout = 0 rvdw = 1.2 -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC

[gmx-users] Temperature decreasing with NVE MARTINI lipid simulation

t = 0 rvdw = 1.2 -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromac

Re: [gmx-users] Different temperatures for different groups, even with Nose-Hoover

On Thu, Oct 29, 2009 at 5:31 PM, XAvier Periole wrote: > > On Oct 29, 2009, at 9:26 PM, Michael Lerner wrote: > > >> I calculated temperatures with >> >> g_traj -f md2.trr -s md2.tpr -n index.ndx -ot -ng 5 >> > I did not know you could get the temperature

Re: [gmx-users] Different temperatures for different groups, even with Nose-Hoover

ke_tol= 0.0001 >> ; Highest order in the expansion of the constraint coupling matrix = >> lincs_order = 4 >> ; Lincs will write a warning to the stderr if in one step a bond = >> ; rotates over more degrees than = >> lincs_warnangle

[gmx-users] Different temperatures for different groups, even with Nose-Hoover

of the time averaged times the instantaneous violation = disre_mixed = no disre_fc = 1000 disre_tau= 1.25 ; Output frequency for pair distances to energy file = nstdisreout = 100 --- end md2.mdp --- -- Michael Lerner, Ph.D. IRTA Pos

Re: [gmx-users] Trying to use g_sas with pbc, also trying to get per-frame output.

On Sun, Jul 19, 2009 at 12:49 PM, David van der Spoel wrote: > Michael Lerner wrote: > >> Hi, >> >> I'm trying to use g_sas on a membrane system. It keeps complaining that >> all of my simulations are done in vacuum (they're not). I poked through >

[gmx-users] Trying to use g_sas with pbc, also trying to get per-frame output.

ike resarea_1.xvg for frame 1, resarea_2.xvg for frame 2, etc. Thanks, -michael -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS) _

[gmx-users] A question about mdrun's input checkpoint file behavior

es the old coordinates. Why doesn't it fail with a warning like "Input checkpoint file not found"? It seems likely to me that most people who specify "-cpi" would prefer the warn-and-fail behavior. Thanks, -Michael -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory

[gmx-users] Can I change xtc-groups while continuing a simulation?

the original coordinates and mdp file to make a phony "initial.tpr" with the new xtc-groups and pass this phony file on to tpbconv. I'm hesitant to do this because I don't actually know what all is in a .tpr file and whether this would cause something to break without a warning.

[gmx-users] Making sure I understand an error

are all either .47 or .37 nm. In the -rdd=1.4 run, the maximum bond lengths range from .68 to .71 nm depending on the particular bond and the A-C distances from the A-B-C triplets range from 1.09 to 1.21. Also, is there any chance that the default settings will get this right for my system in

[gmx-users] Citing the most recent version of GROMACS

t;? (Apologies in advance: I searched the list archives and looked around on the website, but didn't see the answer in an obvious place.) Thanks, -Michael -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314