[gmx-users] GROMACS 2018 first release candidate
Hi GROMACS users, The first release candidate of GROMACS 2018 is available! We plan to make the final release very early in the new year, unless any problems come to light. We are making this available to you to get an early taste of how GROMACS 2018 will look and work, and most importantly to get feedback from you about how well things work. While we try our hardest to keep the quality of GROMACS as high as possible, we’re human, we overlook things while doing other things, and we need your many pairs of eyes to help build a tool that we can all use to do good science! We really need you to test your kinds of simulation on your hardware, both for correctness and performance. This is particularly important if you are using "interesting" hardware or compilers, because we can't test all of them! We've fixed a number of minor issues that users and developers identified - please do try out the new version to see if you agree that things have been fixed where we think they have. No major issues have been identified, which is very good news. See the release notes for details. Please do not use this version for doing science you plan to publish. Similarly, please don’t use this version as a base for a project that bundles or forks GROMACS. What new things can you expect? (See the release notes for more details.) * support for PME running on a GPU * improvements for performance of the short-ranged scheme, particularly on GPUs, through optimizing the pair-list handling * support for the AWH adaptive biasing scheme * new simulation quality checks on physical properties of the integrator * CPU-side enhancements from adding some or better SIMD support to several computations * more reporting of conserved quantities for integrators Just so you know, a fair bit of the work done since 2016 has been re-organizational, rather than new features or faster performance. There’s lots of other new things, and a few old things removed - please see the link to the release notes. All the content of GROMACS 2016.4 and 5.15 is present, apart from features that have been removed. If all goes to plan, we hope to ship the final 2018 release in time for the New Year, but that relies on people joining in and helping us test! We hope you will consider making that contribution, so that we can continue to deliver high-quality free simulation software that will be useful to you in January. You can find the code, manual, release notes, installation instructions and testsuite at the links below. Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2018-rc1.tar.gz Documentation: http://manual.gromacs.org/documentation/2018-rc1/index.html (includes install guide, user guide, reference manual) Release Notes: http://manual.gromacs.org/documentation/2018-rc1/ReleaseNotes/index.html Test Suite: http://gerrit.gromacs.org/download/regressiontests-2018-rc1.tar.gz Happy testing! Mark Abraham GROMACS Development Manager -- 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-requ...@gromacs.org.
[gmx-users] regarding calculation of intra-residue energy
Dear all, I have simulated myoglobin in water system. Now, I want to calculate the self interaction energy (Coulomb) of the protein. In that case shall I consider the interaction between the OE1 and OE2 atoms in glutamte, or other such pairs? Including all pairs, except the bonded pairs, the average self-energy of the protein is coming as 8108 kT from my program. Is this value plausible? Any comment/suggestion is appreciated. Thanks & regards, *Saumyak Mukherjee* Senior Research Fellow, Prof. Biman Bagchi's Lab, Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore - 560012, Karnataka, India. -- 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-requ...@gromacs.org.
[gmx-users] Osmotic Pressure Calculations and fixed reference values of walls
Dear All,
I am performing osmotic pressure simulations using 30 nucleoside molecules
using 1D flat bottom restraints along Z-axis(Zmin and Zmax). I am using
GROMACS 5.0.7 version and reference coordinates are provided using -r
option in grompp.
The osmotic pressure runs are performed under NPT conditions with
semi-isotropic pressure coupling. I am calculating osmotic pressure using
C-program which simply calculates forces on heavy atoms of nucleosides
attempting to cross the Zmin and Zmax limits.
I have searched archived posts, however, I am confused about possible
implementation and post-processing in the present case. Any help will be
really helpful to solve the following issues.
1. The upper and lower limits of the flat bottom restraints are defined
while starting the simulations using static reference frame. Although
|Zmax-Zmin|
will be constant, is it correct to assume fixed minimum(Zmin) and
maximum(Zmax) limits?
2. During post-processing when one centers the trajectory and correct PBC
for nucleoside molecules (trjconv -pbc mol -ur compact -center options), is
it appropriate to assume the same Zmin and Zmax values at t=0 throughout
the analysis?
3. The GROMACS source code section below calculates flat-bottom restraint
forces
for (m = 0; (m < DIM); m++)
{
f[ai][m] += fm[m];
/* Here we correct for the pbc_dx which included rdist */
vir_diag[m] -= 0.5*(dx[m] + rdist[m])*fm[m];
}
How can we print force f[ai][m] at each time step to separate file? I
assume it might be not straightforward to print these forces, but a short
general guideline might help me to achieve the objective.
Sorry for so many questions and Thanks in advance.
Also, Wish you all happy new year in advance.
Best Regards,
Mandar Kulkarni,
Pusan National University, South Korea
--
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-requ...@gromacs.org.
