[gmx-users] 1-4 interaction not within cut-off

[Rabab Toubar]

Hi Justin,

Thanks for the reply. When I tried to gmxcheck the minimization process I got an error:

Timesteps at t=810 don't match (2, 1)

Timesteps at t=814 
don't match (1, 2)

Timesteps at t=816 don't match (2, 1)

Timesteps
 at t=818 don't match (1, 2)

till the end of the run, that is why I thought the system is not properly minimized. I will look into how to check the Potential Energy. 

the em.mdp file is as follows:
cpp          = /usr/bin/cpp ; the c preprocessor
define       = -DFLEXIBLE
constraints  = none
integrator   = steep
dt           = 0.002  ;ps ie 2 fs!
nsteps       = 1000
nstlist      = 10        
ns_type      = grid
rlist         = 1.0     ;short range
coulombtype  = cut-off
rcoulomb     = 1.0     
rvdw         = 1.0
vdwtype      = cut-off  
 fourierspacing  = 0.12
 fourier_nx = 0
 fourier_ny = 0
 fourier_nz = 0
 pme_order = 4
 ewald_rtol = 1e-5
 optimize_fft = yes   
 emtol        = 10   
 emstep       = 0.01

the md.mdp file is:
cpp                 = /usr/bin/cpp 
constraints         =  none                 ;*
integrator          =  md 
dt                  =  0.002  ; ps ! 
nsteps              =   12500000    ; total 25 ns;*
nstcomm             =  1 
nstxout             =  500    ; collect data every 1 ps 
nstvout             =  0 
nstfout             =  0 
nstlist             =  10 
ns_type             =  grid 
rlist               =  1.0 
coulombtype         =  cut-off 
rcoulomb            =  1.0 
vdwtype             =  cut-off 
rvdw                =  1.0            ;*
fourierspacing    =  0.12 
fourier_nx        =  0 
fourier_ny        =  0 
fourier_nz        =  0 
pme_order         =  4 
ewald_rtol        =  1e-5 
optimize_fft            =  yes      

; Berendsen temperature coupling is on 
Tcoupl                =  berendsen 
tau_t                 =  0.1    0.1 
tc-grps               =      protein    non-protein  
ref_t                 =  300        300 

; Pressure coupling is on
Pcoupl              =  berendsen
pcoupltype        =  isotropic
tau_p               =  0.5    ; ps
compressibility     =  4.5e-5    ; bar-1
ref_p               =  1.0

; Generate velocites is on at 300 K. 
gen_vel             =  yes
gen_temp            =  300.0 
gen_seed            = 621432

Any suggestions are appreciated

Thanks
Rabab Toubar


--- On Thu, 6/3/10, Justin A. Lemkul <jalemkul at vt.edu> wrote:

From: Justin A. Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] 1-4 interaction not within cut-off
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Thursday, June 3, 2010, 4:37 PM



Rabab Toubar wrote:
> Hi,
> 
> I set my .mdp file to minimize the system for 1000 steps, but it stopped at ~200 saying: "Stepsize too
 small, or no change in energy.
> Converged to machine precision, but not to the requested precision Fmax < 10" but the molecule is now outside the box
> 

This is not really a problem, provided that both the potential energy and Fmax that resulted are reasonable.http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision

> I did position restraint for 2ns using LINCS, and things went well
> 
> running md, it ran for only 0.3 ns out of 30, and I got an error message that 1-4 interaction between 2 atoms are at a distance > table-size (1nm) with a suggestion to increase the table-extension in mdp file.
> I checked  http://www.gromacs.org/Documentation/Errors#1-4_interaction_not_within_cut-off suggesting reminimizing.
> 

The other possibility is that your .mdp settings are inappropriate, but you haven't provided that information.

> My question is: is it OK that the system doesn't minimize till the end of the specified number of steps? is it OK to be outside the box as long as you assign boundary conditions as in case of NAMD? and what is the best option - you think - I have to solve the md problem
> 

Whether or not you need to revisit the EM procedure depends on how well it actually did (see comment above).  The periodicity effect is a non-issue, since there is no "outside" of a periodic box.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-Justin

> Any suggestions are highly apprecitaed
> Rabab
> 
> 

-- ========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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