[gmx-users] mixed, double precision
peter.stern at weizmann.ac.il
Mon Feb 20 12:58:02 CET 2017
I think so. There is not much meaning to the input/output precision since no coordinates are more than single precision. The purpose of double precision is to prevent computational errors arising from accumulated roundoff errors, for example, in normal mode analysis where computations involving large matrices are required. But by the same token, such a series of runs may not be reproducible.
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Joel Markgren
Sent: Monday, February 20, 2017 1:09 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] mixed, double precision
Gooday dear Gromacs users,
I have access to a 5.1.4 version of gromacs compiled in double precision on a cluster.
I equilibrated a couple of samples for NVT and NPT and used following commands: (the ... means that the rest of the input commands are not relevant for the question).
gmx_mpi grompp ... -o nvt.tpr
gmx_mpi_d mdrun -v -deffnm nvt
gmx_mpi grompp ... -c nvt.gro -o npt.tpr
gmx_mpi_d mdrun -v -deffnm
I realized after the runs that I forgot to specify that I wish to use the grompp commands in double precision (gmx_mpi_d grompp).
Have I understood it correctly, that when grompp receives input from a run made in double precision, it will produce an output in mixed precision, if not specified to do it in double precision? When the mdrun gets the input which is in mixed precision it will still make the run in double precision even if the input is in mixed.
Have I lost some of the precision between the runs, with risks of energy drifts?
I see it's a bit messy but I hope you understand. Please let me know if you need more info or clarifications to answer my question.
Thanks in advance for taking you time to answer my questions.
PhD student in Biology
Swedish University of Agricultural Sciences
Department of Plant Breeding
PO Box 101, Sweden 23053 Lund
Visiting address: Sundsvägen 10, 23053 Lund
Mobile: +46 706101128
joel.markgren at slu.se, www.slu.se<http://www.slu.se/> [https://internt.slu.se/PageFiles/81117/SLU_Logo_mail.png]
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