[gmx-users] Problem to run more than 2 NPT REMD replicas

[David van der Spoel]

pascal.baillod at epfl.ch wrote:

>Dear REMD users and developers,
>
>
>I still do not manage to get PT running with more than 2 replicas, in the
>NPT ensemble.. For reminder:
>
>I have tried running NPT-REMD with 3 replicas, at 300, 302 and 304 K. My .mdp
>files are identical, with the exception of the target temperature. I
>systematically get the following error message:
>
>
>
>++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>T. Okabe and M. Kawata and Y. Okamoto and M. Mikami
>Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
>Chem. Phys. Lett. 335 (2001) pp. 435-439
>-------- -------- --- Thank You --- -------- --------
>                                                                               
>                               
>Multi-checking the number of atoms ... OK
>Multi-checking the integrator ... OK
>Multi-checking nsteps ... OK
>Multi-checking init_step ... OK
>Multi-checking the temperature coupling ... OK
>Multi-checking the number of temperature coupling groups ... OK
>Multi-checking the pressure coupling ... OK
>Repl  There are 3 replicas:
>Repl      0     1     2
>Repl  T 300.0 302.0 304.0
>Repl  p  1.00  1.00  2.00-------------------------------------------------------
>Program mdrun_mpi, VERSION 3.3
>Source code file: repl_ex.c, line: 142
>                                                                               
>                               
>Fatal error:
>The reference pressure decreases with increasing temperature
>-------------------------------------------------------
>  
>
It seems that your pressure*increases* with increasing temperature.
Check line 141 in src/kernel/repl_ex.c
it should read:

    if ((i > 0) && (re->pres[re->ind[i]] < re->pres[re->ind[i-1]]))
      gmx_fatal(FARGS,"The reference pressure decreases with increasing 
temperature");

Check whether you have < or >

>                                                                               
>                               
>"Smileys are Not Cool" (D. Van Der Spoel)
>
>
>As you can see from the log file above, I set the target pressure from the 3rd
>replica to 2 bar, just to check out the "fatal error" statement. As additional
>tests, I 
>
>1) prepared the tpr files after removing the pressure keywords in the .mdp input
>files, in order to try NVT REMD. This worked out fine, for the same initial
>replicas.
>
>2) Tried the same for a small peptide solvated in water, where the replicas were
>already pre-equilibrated to the target tempertature. This gave the same error
>message. 
>
>Below, follows a copy of one of my 3 .mdp files, the other 2 being identical
>with the exception of the target temperature and/or target pressure.
>
>
>title                    =  
>cpp                      = /lib/cpp
>include                  = -I../top
>define                   = 
>
>integrator               = md
>dt                       = 0.0015
>tinit                    = 0.0     
>nsteps                   = 2000000  
>comm_mode       	 = Linear               
>nstcomm                  = 1       5
>comm_grps                = Protein Other
>nstxout                  = 5000             
>nstvout                  = 5000                    
>nstlog                   = 10 		      
>nstenergy                = 10 		
>nstxtcout                = 500           
>xtc_grps		 =              
>energygrps               = Protein Other
>
>
>nstlist                  = 10
>ns_type                  = grid
>rlist                    = 1.0
>coulombtype              = PME
>rcoulomb-switch          = 0
>rcoulomb                 = 1.0
>rvdw                     = 1.0
>fourierspacing           = 0.12
>fourier_nx               = 64
>fourier_ny               = 64
>fourier_nz               = 64
>pme_order                = 4
>ewald_rtol               = 1e-5
>ewald_geometry           = 3d
>epsilon_surface          = 0
>optimize_fft             = no
>
>tcoupl                   = berendsen
>tc-grps                  = Protein Other  
>tau_t                    = 0.1     0.4   
>ref_t                    = 300.0  300.0
>Pcoupl                   = berendsen
>pcoupltype               = isotropic
>tau_p                    = 1.0
>compressibility          = 4.5e-5
>ref_p                    = 1.0
>
>constraints              = none   
>constraint_algorithm     = 
>unconstrained-start      = 
>shake_tol                = 1e-04
>morse                    = no
>
>gen_vel                  = no
>
>
>Dose anybody have a clue of what is going on? Many thanks in advance!
>
>
>Pascal
>
>
>
>
>*******************************************************************************
>Pascal Baillod (PhD student) 
>*******************************************************************************
>Swiss Federal Institute of Technology EPFL	        Tel: +41-(0)21-693-0322
>Institute of Chemical Sciences and Engineering ,	Fax: +41-(0)21-693-0320
>Laboratory of Computational Chemistry and Biochemistry	pascal.baillod at epfl.ch
>Room BCH 4121, Avenue Forel,	                        http://lcbcpc21.epfl.ch
>CH-1015 Lausanne	
>*******************************************************************************
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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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