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

#SUKRITI GUPTA# SUKRITI002 at e.ntu.edu.sg
Sun Dec 18 07:25:43 CET 2016 

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.

More information about the gromacs.org_gmx-users mailing list