[gmx-users] restraint/freeze issues
David van der Spoel
spoel at xray.bmc.uu.se
Fri Nov 19 10:19:11 CET 2004
On Thu, 2004-11-18 at 16:47 -0500, Ken Rotondi wrote:
> Hello all,
> I'm having problems with position restraints. I'm trying test
> simulations of a tripeptide with the Calpha of residue 1 restrained
> with x,y,z constants of 10,000 each. When I run gmxdump on my .tpr file
> I find the following:
> functype=POSRES, pos0A=( 2.01600003e+00, 1.98000002e+00,
> 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00),
> pos0B=( 2.01600003e+00, 1.98000002e+00, 0.00000000e+00), fcB=(
> 0.00000000e+00, 0.00000000e+00, 0.00000000e+00)
> functype=POSRES, pos0A=( 1.60999998e-01,
> 1.99699998e+00, 0.00000000e+00), fcA=( 1.00000000e+04, 1.00000000e+04,
> 1.00000000e+04), pos0B=( 1.60999998e-01, 1.99699998e+00,
> 0.00000000e+00), fcB=( 1.00000000e+04, 1.00000000e+04, 1.00000000e+04)
> functype=POSRES, pos0A=( 1.99000001e-01,
> 1.43000007e-01, 0.00000000e+00), fcA=( 0.00000000e+00, 0.00000000e+00,
> 0.00000000e+00), pos0B=( 1.99000001e-01, 1.43000007e-01,
> 0.00000000e+00), fcB=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00)
> so yes, the appropriate atom is restrained. However, when I preform a
> 50ps simulation at 400K the peptide just vibrates. Similar behavior was
> seen on a longer peptide simulated at 500K for 3ns, which prompted
> these tests. Upon looking through the gmxdump of my test .tpr file I
> found this at the end:
> Group statistics
> T-Coupling : 26 627 1 (total 654 atoms)
> Energy Mon. : 26 627 1 (total 654 atoms)
> Acceleration: 654 (total 654 atoms)
> Freeze : 654 (total 654 atoms)
> User1 : 654 (total 654 atoms)
> User2 : 654 (total 654 atoms)
> VCM : 654 (total 654 atoms)
> XTC : 26 628 (total 654 atoms)
> Or. Res. Fit: 654 (total 654 atoms)
> Question 1) How do I group the CL- (1) with the SOL (627) in the same
> temperature bath, as Xavier has suggested?
make a new group with make?ndx
> Question 2) Does the "Freeze : 654 (total 654 atoms)" entry indicate
> that my system is indeed frozen?
depends on the freezing parameters. most likely not since this is your
> Question 3) If the answer to question 2 is negative, what is a next
> logical step?
What do you mean? The one atom is restrained and the rest won't be able
to move very far, so yes, your peptide will vibrate
> I include my .mdp file for a slightly longer test run. I see nothing
> unusual about it, but perhaps clearer eyes...
> As always, many thanks,
> ; .mdp file for NVT test MD of peptide fragments
> ; 0.2 ns
> ; User Ken
> ; Wed Nov 18 11:22:44 2004
> ; Input file
> title = Chicken
> cpp = /lib/cpp
> define = -DPOSRES
> constraints = h-bonds
> integrator = md
> dt = 0.002 ; ps !
> nsteps = 100000 ; total 0.2 ns.
> nstxout = 5000 ; cord to .trr file every 10 ps.
> nstvout = 5000 ; velo to .trr file every 10 ps.
> nstfout = 5000 ; force to .trr file every 10 ps.
> nstlog = 5000 ; energ to log file every 10ps.
> nstenergy = 250 ; energ to energ file every 0.5ps
> nstxtcout = 250 ; cood to .xtc file every 0.5ps
> xtc_grps = Protein
> nstlist = 10 ; freq (steps) update neighbor list
> ns_type = grid
> pbc = xyz ; turns on periodic bound. cond.
> rlist = 0.95
> coulombtype = switch
> rcoulomb = 0.9
> rcoulomb_switch = 0.7
> vdwtype = switch
> rvdw = 0.9
> rvdw_switch = 0.7
> ; Nose-Hover temperature coupling is on in three groups
> tcoupl = nose-hoover
> tc_grps = Protein SOL CL-
> tau_t = 0.1 0.1 0.1
> ref_t = 408 408 408
> ; Energy monitoring
> energygrps = Protein SOL CL-
> ; Generate velocites is on at 408 K.
> gen_vel = yes
> gen_temp = 408.0
> gen_seed = -1
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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