[gmx-users] restraint/freeze issues

[David van der Spoel]

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[100]=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[101]=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[102]=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)
> etc.
> 
> 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
entire system
> 
> 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,
> 
> Ken
> 
> ;       .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.
________________________________________________________________________
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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