[gmx-users] Problem in running energy minimization in Gromacs 5.1.2 version
Mark Abraham
mark.j.abraham at gmail.com
Sun Dec 18 09:05:13 CET 2016
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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