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Bug #1640

Continuation of Simulation of Potential-shift-Verlet Potential Modifiers has Sharp Rise of Total Energy Near Step 0

Added by Johnny Lu almost 5 years ago. Updated about 4 years ago.

Status:
Closed
Priority:
Normal
Assignee:
-
Category:
-
Target version:
-
Affected version - extra info:
GPU. The machine has 4 GPU, and I used them.
Affected version:
Difficulty:
uncategorized
Close

Description

Problem
NPT14 and NPT15 uses the same mdp file, except that NPT15 has a nsteps that
is 300,000,000, which is 10 times larger than that of NPT14.

NPT15 continues from NPT14. NPT15 very qucikly see a rise in total energy
from the total energy at the end of NPT14.(see the xvg file)
Both NPT14 and NPT15 uses the shift potential modifier for VdW and PME,
were ran on the same machine with GPU.

NPT15 Total Energy:

  1. This file was created Tue Nov 11 02:32:40 2014
  2. by the following command:
  3. g_energy -f npt15.edr -o ../npt15_energy.xvg #
  4. g_energy is part of G R O M A C S: #
  5. God Rules Over Mankind, Animals, Cosmos and Such #
    title "Gromacs Energies"
    xaxis label "Time (ps)"
    yaxis label "(kJ/mol)"
    @TYPE xy
    view 0.15, 0.15, 0.75, 0.85
    legend on
    legend box on
    legend loctype view
    legend 0.78, 0.8
    legend length 2
    s0 legend "Total Energy"
    0.000000 -402120.187500
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small_files.tar.gz (2.84 MB) small_files.tar.gz Johnny Lu, 11/11/2014 07:34 PM
WhatHappened.txt (2.87 KB) WhatHappened.txt Johnny Lu, 11/11/2014 07:36 PM

History

#1 Updated by Johnny Lu over 4 years ago

When I constrained the H-bonds with lincs. This behavior seems to disappear on an alanine tripeptide simulation that I ran.

#2 Updated by Erik Lindahl about 4 years ago

  • Status changed from New to Feedback wanted

Hi Johnny,

Please check if this is still a problem for the latest version of Gromacs 5.0.

#3 Updated by Erik Lindahl about 4 years ago

  • Status changed from Feedback wanted to Rejected

This bug report does not contain enough files to confirm that it is an issue. Feel free to reopen when you include both the initial coordinates and topology, so that it is possible to reproduce on the latest version of Gromacs-5.0 by running grompp and mdrun.

#4 Updated by Erik Lindahl about 4 years ago

  • Status changed from Rejected to Closed

Cannot reproduce any bug with a simple water system when just running 1000 steps. A quick look at the files indicated that the coulomb settings change from switch to shift between npt13 and npt14, which will obviously affect energy.

PS: If you want to reopen, avoid uploading files that would require running 300 million steps - no developer is going to bother with that. An ideal bug report should be a tiny system (10 atoms is wonderful, 1000-10,000 OK) where there is a clear difference after 1 step depending on settings.

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