[gmx-users] limitations in tau_t and ref_t values

[David van der Spoel]

On Mon, 2005-05-16 at 20:18 -0300, Monique Brito wrote:
> Hi, people!
> 
> I´m doing the simulation in vacuo, then I have no
> ions.
> Below I send the md.mdp file.
> The Index file has Protein_A, Protein_B, MKC and
> all  residues seen in the md.mdp file.
> I want to find the lennard-jones and coulomb
> interactions between the ligand MKC and the
> residues shown below.
> When I run grompp, gromacs return an error, it
> says "there is 56 groups, but only 22 tau_t and
> ref_t values". But I have put all values! Are
> there some limitations in the number of tc_grps
> groups?
Max 256 groups. Do you have all that on one line without line breaks?


> Thanks,
> Monique Brito
> 
> md.mdp
> 
> title                    = 1rt1
> include                  =
> define                   =
> integrator               = md
> dt                       = 0.001   ; 1 fs time
> step
> nsteps                   = 1000000 ; 1000 ps
> simulation
> nstxout                  = 500
> nstvout                  = 500
> nstlog                   = 500
> nstenergy                = 50
> nstxtcout                = 0
> energygrps               = MKC Protein_A
> Protein_B r_94 r_95 r_96 r_97 r_98 r_99 r_100
> r_101 r_102 r_103 r_104 r_105 r_106 r_107 r_108
> r_178 r_179 r_180 r_181 r_182 r_183 r_186 r_187
> r_188 r_189 r_190 r_191 r_192 r_198 r_223 r_224
> r_225 r_226 r_227 r_228 r_229 r_230 r_232 r_233
> r_234 r_235 r_236 r_237 r_238 r_239 r_240 r_317
> r_318 r_319 r_136 r_137 r_138 r_139
> nstlist                  = 10  ; default value
> ns_type                  = grid
> rlist                    = 0.8
> pbc                      = xyz
> coulombtype              = PME
> pme_order                = 4
> optimize_fft             = yes
> rcoulomb                 = 1.0
> rvdw                     = 0.8
> xtc_grps                 = MKC Protein_A
> Protein_B r_94 r_95 r_96 r_97 r_98 r_99 r_100
> r_101 r_102 r_103 r_104 r_105 r_106 r_107 r_108
> r_178 r_179 r_180 r_181 r_182 r_183 r_186 r_187
> r_188 r_189 r_190 r_191 r_192 r_198 r_223 r_224
> r_225 r_226 r_227 r_228 r_229 r_230 r_232 r_233
> r_234 r_235 r_236 r_237 r_238 r_239 r_240 r_317
> r_318 r_319 r_136 r_137 r_138 r_139
> tcoupl                   = Berendsen
> tc-grps                  = MKC Protein_A
> Protein_B r_94 r_95 r_96 r_97 r_98 r_99 r_100
> r_101 r_102 r_103 r_104 r_105 r_106 r_107 r_108
> r_178 r_179 r_180 r_181 r_182 r_183 r_186 r_187
> r_188 r_189 r_190 r_191 r_192 r_198 r_223 r_224
> r_225 r_226 r_227 r_228 r_229 r_230 r_232 r_233
> r_234 r_235 r_236 r_237 r_238 r_239 r_240 r_317
> r_318 r_319 r_136 r_137 r_138 r_139
> tau_t                    = 0.1 0.1       0.1     
> 0.1  0.1  0.1  0.1  0.1  0.1  0.1   0.1   0.1  
> 0.1   0.1   0.1   0.1   0.1   0.1   0.1   0.1  
> 0.1   0.1
> 0.1   0.1   0.1   0.1   0.1   0.1   0.1   0.1  
> 0.1   0.1   0.1   0.1   0.1
> 0.1   0.1   0.1   0.1   0.1   0.1   0.1   0.1  
> 0.1   0.1   0.1   0.1   0.1
> 0.1   0.1   0.1   0.1   0.1   0.1   0.1   0.1
> ref_t                    = 300 300       300     
> 300  300  300  300  300  300  300   300   300  
> 300   300   300   300   300   300   300   300  
> 300   300
> 300   300   300   300   300   300   300   300  
> 300   300   300   300   300
> 300   300   300   300   300   300   300   300  
> 300   300   300   300   300
> 300   300   300   300   300   300   300   300
> Pcoupl                   = Berendsen
> tau_p                    = 1.0
> compressibility          = 4.5e-5
> ref_p                    = 1.0
> gen_vel                  = yes
> gen_temp                 = 300
> gen_seed                 = 173529
> constraints              = none
> 
> 
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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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