[gmx-users] Problem in running energy minimization in Gromacs 5.1.2 version

Mark Abraham mark.j.abraham at gmail.com
Sun Dec 18 09:12:53 CET 2016 

Hi,

All I know is that you've reported that nothing is obviously wrong :-)

Mark

On Sun, 18 Dec 2016 19:10 #SUKRITI GUPTA# <SUKRITI002 at e.ntu.edu.sg> wrote:

> Hi Mark,
>
>
> Thanks for the prompt reply. So continuing with the same shouldn't be an
> issue right?
>
> Regards
>
> Sukriti
> [
> https://sixprd0111.outlook.com/owa/service.svc/s/GetFileAttachment?id=AAMkADNjYmY4NDc0LTVjMzUtNDNmOC1hYzdkLTU5NTZhODkwYjVhNwBGAAAAAACBUPJnHBz9Qb1jEGoiHu01BwCW%2B40K8EMKR52f2bViS6X0AAAANaBFAAC1PvQTaUN0S5CzEDGS8lwUAAIr8o3VAAABEgAQAIhFug57qj9Lg6WQKih11Lg%3D&X-OWA-CANARY=h9cz1GMp80awqK7uWU0tmwAfbhpQFtMYCkfwOWcjFqjCjKA5rnYYMRF4FV7Oec3YWfk_SWGzz4s.&retryCount=3
> ]
>
> Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI at N)
> | Nanyang Technological University
> N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798
> Tel: (65) 81164191 GMT+8h | Email:sukriti002 at e.ntu.edu.sg | Web:
> erian.ntu.edu.sg<http://www.ntu.edu.sg/home/xuzc/People.html>
>
>
>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mark
> Abraham <mark.j.abraham at gmail.com>
> Sent: Sunday, December 18, 2016 4:04:59 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Problem in running energy minimization in Gromacs
> 5.1.2 version
>
> Hi,
>
> Well that is fine. You were presumably running a minimisation to relax the
> structure to permit things to run. That a different path for minimisation
> didn't work is not necessarily of interest.
>
> Mark
>
> On Sun, 18 Dec 2016 19:01 #SUKRITI GUPTA# <SUKRITI002 at e.ntu.edu.sg> wrote:
>
> > Hi Mark,
> >
> >
> > When I complete energy minimization in version 4.5.5, I am able to run
> npt
> > and nvt runs in new version i.e. 5.1.2.
> >
> >
> > Regards
> >
> > Sukriti
> > [
> >
> https://sixprd0111.outlook.com/owa/service.svc/s/GetFileAttachment?id=AAMkADNjYmY4NDc0LTVjMzUtNDNmOC1hYzdkLTU5NTZhODkwYjVhNwBGAAAAAACBUPJnHBz9Qb1jEGoiHu01BwCW%2B40K8EMKR52f2bViS6X0AAAANaBFAAC1PvQTaUN0S5CzEDGS8lwUAAIr8o3VAAABEgAQAIhFug57qj9Lg6WQKih11Lg%3D&X-OWA-CANARY=h9cz1GMp80awqK7uWU0tmwAfbhpQFtMYCkfwOWcjFqjCjKA5rnYYMRF4FV7Oec3YWfk_SWGzz4s.&retryCount=3
> > ]
> >
> > Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI at N
> )
> > | Nanyang Technological University
> > N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798
> > Tel: (65) 81164191 GMT+8h | Email:sukriti002 at e.ntu.edu.sg | Web:
> > erian.ntu.edu.sg<http://www.ntu.edu.sg/home/xuzc/People.html>
> >
> >
> >
> > ________________________________
> > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mark
> > Abraham <mark.j.abraham at gmail.com>
> > Sent: Sunday, December 18, 2016 3:29:31 PM
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Problem in running energy minimization in
> Gromacs
> > 5.1.2 version
> >
> > Hi,
> >
> > You have a minimized structure (somehow). What happens when you use it as
> > the starting point in the newer version?
> >
> > Mark
> >
> > On Sun, 18 Dec 2016 17:26 #SUKRITI GUPTA# <SUKRITI002 at e.ntu.edu.sg>
> wrote:
> >
> > > Hi,
> > >
> > >
> > > Can anyone please help.
> > >
> > >
> > > Regards
> > >
> > > Sukriti
> > >
> > > [
> > >
> >
> https://sixprd0111.outlook.com/owa/service.svc/s/GetFileAttachment?id=AAMkADNjYmY4NDc0LTVjMzUtNDNmOC1hYzdkLTU5NTZhODkwYjVhNwBGAAAAAACBUPJnHBz9Qb1jEGoiHu01BwCW%2B40K8EMKR52f2bViS6X0AAAANaBFAAC1PvQTaUN0S5CzEDGS8lwUAAIr8o3VAAABEgAQAIhFug57qj9Lg6WQKih11Lg%3D&X-OWA-CANARY=h9cz1GMp80awqK7uWU0tmwAfbhpQFtMYCkfwOWcjFqjCjKA5rnYYMRF4FV7Oec3YWfk_SWGzz4s.&retryCount=3
> > > ]
> > >
> > > Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU
> (ERI at N
> > )
> > > | Nanyang Technological University
> > > N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798
> > > Tel: (65) 81164191 GMT+8h | Email:sukriti002 at e.ntu.edu.sg | Web:
> > > erian.ntu.edu.sg<http://www.ntu.edu.sg/home/xuzc/People.html>
> > >
> > >
> > >
> > > ________________________________
> > > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> > > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of
> #SUKRITI
> > > GUPTA# <SUKRITI002 at e.ntu.edu.sg>
> > > Sent: Friday, December 16, 2016 4:27:41 PM
> > > To: gromacs.org_gmx-users at maillist.sys.kth.se
> > > Subject: [gmx-users] Problem in running energy minimization in Gromacs
> > > 5.1.2 version
> > >
> > > This sender failed our fraud detection checks and may not be who they
> > > appear to be. Learn about spoofing at http://aka.ms/LearnAboutSpoofing
> > >
> > > Dear all,
> > >
> > >
> > > I was running my gromacs simulations on Gromacs 4.5.5 version but my
> > > system got updated and it changed to Gromacs 5.1.2. No when I run the
> > same
> > > energy minimization file as earlier but just adding cutoff-scheme =
> > Verlet,
> > > my energy minimization is not running. Following is the message I get
> > from
> > > Gromacs:
> > >
> > >
> > > Low-Memory BFGS Minimizer:
> > >    Tolerance (Fmax)   =  1.00000e+01
> > >    Number of steps    =         5000
> > > Using 10 BFGS correction steps.
> > >
> > >    F-max             =  2.21705e+05 on atom 295
> > >    F-Norm            =  1.25724e+04
> > >
> > > Step 0, Epot=1.569290e+03, Fnorm=8.461e+03, Fmax=1.134e+05 (atom 295)
> > >
> > > Energy minimization has stopped, but the forces have not converged to
> the
> > > requested precision Fmax < 10 (which may not be possible for your
> > system).
> > > It
> > > stopped because the algorithm tried to make a new step whose size was
> too
> > > small, or there was no change in the energy since last step. Either
> way,
> > we
> > > regard the minimization as converged to within the available machine
> > > precision, given your starting configuration and EM parameters.
> > >
> > > Double precision normally gives you higher accuracy, but this is often
> > not
> > > needed for preparing to run molecular dynamics.
> > >
> > > writing lowest energy coordinates.
> > >
> > > Back Off! I just backed up v_b4pr.gro to ./#v_b4pr.gro.3#
> > >
> > > Low-Memory BFGS Minimizer converged to machine precision in 0 steps,
> > > but did not reach the requested Fmax < 10.
> > > Potential Energy  =  1.5692902e+03
> > > Maximum force     =  1.1339475e+05 on atom 295
> > > Norm of force     =  8.4610078e+03
> > >
> > > NOTE: 18 % of the run time was spent in pair search,
> > >       you might want to increase nstlist (this has no effect on
> accuracy)
> > >
> > > However, if I run energy minimization of the same file in version
> 4.5.5,
> > > energy minimization takes place and I do not encounter any error. Can
> > > anyone please help me with this? My energy minimization mdp file is as
> > > follows:
> > >
> > > ; VARIOUS PREPROCESSING OPTIONS
> > > title                    =
> > > cpp                      = /lib/cpp
> > > include                  =
> > > define                   = -DFLEXIBLE
> > >
> > > ; RUN CONTROL PARAMETERS
> > > integrator               = l_bfgs
> > > ; Start time and timestep in ps
> > > tinit                    = 0
> > > dt                       = 0.001
> > > nsteps                   = 5000
> > > ; For exact run continuation or redoing part of a run
> > > init_step                = 0
> > > ; mode for center of mass motion removal
> > > comm-mode                = Linear
> > > ; number of steps for center of mass motion removal
> > > nstcomm                  = 1
> > >
> > > ; ENERGY MINIMIZATION OPTIONS
> > > ; Force tolerance and initial step-size
> > > emtol                    = 10
> > > emstep                   = 0.01
> > > ; Max number of iterations in relax_shells
> > > niter                    = 20
> > > ; Step size (1/ps^2) for minimization of flexible constraints
> > > fcstep                   = 0
> > > ; Frequency of steepest descents steps when doing CG
> > > nstcgsteep               = 1000
> > > nbfgscorr                = 10
> > >
> > > ; OUTPUT CONTROL OPTIONS
> > > ; Output frequency for coords (x), velocities (v) and forces (f)
> > > nstxout                  = 100
> > > nstvout                  = 100
> > > nstfout                  = 100
> > > ; Checkpointing helps you continue after crashes
> > > nstcheckpoint            = 1000
> > > ; Output frequency for energies to log file and energy file
> > > nstlog                   = 100
> > > nstenergy                = 100
> > > ; Output frequency and precision for xtc file
> > > nstxtcout                = 0
> > > xtc-precision            = 1000
> > > ; This selects the subset of atoms for the xtc file. You can
> > >
> > > ; NEIGHBORSEARCHING PARAMETERS
> > > ; nblist update frequency
> > > cutoff-scheme = Verlet
> > > nstlist                  = 10
> > > ; ns algorithm (simple or grid)
> > > ns-type                  = Grid
> > > ; Periodic boundary conditions: xyz (default), no (vacuum)
> > > ; or full (infinite systems only)
> > > pbc                      = xyz
> > > ; nblist cut-off
> > > rlist                    = 1.1
> > > domain-decomposition     = no
> > >
> > > ; OPTIONS FOR ELECTROSTATICS AND VDW
> > > ; Method for doing electrostatics
> > >
> > > coulombtype              = PME
> > > rcoulomb                 = 1.1
> > > ; Method for doing Van der Waals
> > > vdw-type                 = Switch
> > > ; cut-off lengths
> > > rvdw-switch              = 0.8
> > > rvdw                     = 1.1
> > > ; Apply long range dispersi0n corrections for Energy and Pressure
> > > DispCorr                 = No
> > > ; Extension of the potential lookup tables beyond the cut-off
> > > table-extension          = 2
> > > ; Spacing for the PME/PPPM FFT grid
> > > fourierspacing           = 0.12
> > > ; FFT grid size, when a value is 0 fourierspacing will be used
> > > fourier_nx               = 0
> > > fourier_ny               = 0
> > > fourier_nz               = 0
> > > ; EWALD/PME/PPPM parameters
> > > pme_order                = 4
> > > ewald_rtol               = 4e-05
> > > ewald_geometry           = 3d
> > >
> > > epsilon_surface          = 0
> > > optimize_fft             = no
> > >
> > > ; GENERATE VELOCITIES FOR STARTUP RUN
> > > gen-vel                  = no
> > > gen-temp                 = 300
> > > gen-seed                 = 173529
> > >
> > > freezegrps = V
> > > freezedim = Y Y Y
> > >
> > >
> > >
> > > Thanks and Regards
> > >
> > >
> > > Sukriti
> > >
> > > [
> > >
> >
> https://sixprd0111.outlook.com/owa/service.svc/s/GetFileAttachment?id=AAMkADNjYmY4NDc0LTVjMzUtNDNmOC1hYzdkLTU5NTZhODkwYjVhNwBGAAAAAACBUPJnHBz9Qb1jEGoiHu01BwCW%2B40K8EMKR52f2bViS6X0AAAANaBFAAC1PvQTaUN0S5CzEDGS8lwUAAIr8o3VAAABEgAQAIhFug57qj9Lg6WQKih11Lg%3D&X-OWA-CANARY=h9cz1GMp80awqK7uWU0tmwAfbhpQFtMYCkfwOWcjFqjCjKA5rnYYMRF4FV7Oec3YWfk_SWGzz4s.&retryCount=3
> > > ]
> > >
> > > Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU
> (ERI at N
> > )
> > > | Nanyang Technological University
> > > N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798
> > > Tel: (65) 81164191 GMT+8h | Email:sukriti002 at e.ntu.edu.sg | Web:
> > > erian.ntu.edu.sg<http://www.ntu.edu.sg/home/xuzc/People.html>
> > >
> > >
> > >
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