[gmx-users] Enthalpy calculation in NPT ensemble

Pelin S Bulutoglu pbulutog at purdue.edu
Tue Aug 14 22:32:46 CEST 2018

Dear David,

Thanks a lot for your reply. I am using GROMACS version 2016.5. I performed isotropic pressure coupling for 4 ns followed by anisotropic pressure coupling for another 4 ns. I actually realized that the enthalpy and PV options are available when the pressure is coupled isotropically, but not when it is coupled anisotropically. Any input on why this may happen would be greatly appreciated.


Pelin Su Bulutoglu

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of David van der Spoel <spoel at xray.bmc.uu.se>
Sent: Tuesday, August 14, 2018 2:11:58 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Enthalpy calculation in NPT ensemble

Den 2018-08-14 kl. 16:07, skrev Pelin S Bulutoglu:
> Dear GROMACS users,
> I am working on simulating a glycine crystal using GAFF force field with CNDO point charges in an NPT ensemble. I want to calculate the enthalpy and Cp of the crystal. However, the list that comes up following gmx energy command does not include the enthalpy or PV options, as it would normally do for NPT simulations. Does this mean that the simulation does not exhibit NPT behavior? I believe that this is not the case, since upon inspection of the temperature and pressure values, I found that they are both constant (within statistical error) throughout the simulation. What may be the cause of this? The following are some of my input parameters:
>     cutoff-scheme                  = Verlet
>     nstlist                        = 40
>     ns-type                        = Grid
>     pbc                            = xyz
>     verlet-buffer-tolerance        = 0.005
>     rlist                          = 1.4
>     coulombtype                    = PME
>     coulomb-modifier               = Potential-shift
>     rcoulomb-switch                = 0
>     rcoulomb                       = 1.4
>     rvdw                           = 1.4
>     DispCorr                       = EnerPres
>     table-extension                = 1
>     fourierspacing                 = 0.12
>     pme-order                      = 4
>     tcoupl                         = V-rescale
>     nsttcouple                     = 10
>     pcoupl                         = Berendsen
>     pcoupltype                     = Anisotropic
>     nstpcouple                     = 10
>     tau-p                          = 2
>     compressibility (3x3):
>        compressibility[    0]={ 4.50000e-05,  4.50000e-05,  4.50000e-05}
>        compressibility[    1]={ 4.50000e-05,  4.50000e-05,  4.50000e-05}
>        compressibility[    2]={ 4.50000e-05,  4.50000e-05,  4.50000e-05}
>     ref-p (3x3):
>        ref-p[    0]={ 1.00000e+00,  1.00000e+00,  1.00000e+00}
>        ref-p[    1]={ 1.00000e+00,  1.00000e+00,  1.00000e+00}
>        ref-p[    2]={ 1.00000e+00,  1.00000e+00,  1.00000e+00}
>     refcoord-scaling               = COM
> Any input would be greatly appreciated. Thanks in advance.
> Pelin Su Bulutoglu
The enthalpy should be there with any modern gromacs version if you are
using constant pressure simulations. Please double check gmx energy
options. Cp is more tricky because you need quantum corrections.

David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.

Institutionen för cell- och molekylärbiologi ...<http://www.icm.uu.se/>
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