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

#SUKRITI GUPTA# SUKRITI002 at e.ntu.edu.sg
Sun Dec 18 09:01:27 CET 2016 

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>
>
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list