[gmx-users] how to calculate binding energy using MMPBSA

Dear users I have run a MD simulation 50 ns and I am going to calculate the binding energy of DNA-ligand complex using MMPBSA, but I do not know how to do this, I appreciate any suggestion. Best Regards Maryam -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] System has non-zero total charge

http://www.gromacs.org/Documentation/Errors#System_has_non-zero_total_charge "If the charge is already close to an integer, then the difference is caused by rounding errors and not a major problem." If want to pursue further, there are discussions and comments by developers on this emailing list

Re: [gmx-users] High pressure variation during NPT equilibration of Protein-ligand system.

For some examples, see: https://twitter.com/dr_dbw/status/968624615063937025 Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu

Re: [gmx-users] Regarding to find coordination number

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-May/125328.html Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu

[gmx-users] System has non-zero total charge

Hi, Running grompp I get the NOTE "System has non-zero total charge: 0.000180". I have been running this electrolyte system which includes multiple molecules before without a problem. There are ions in the system as well as polar molecules (via atomic partial charges). The total charge of each

Re: [gmx-users] Error when using mdrun_mpi

Hi, Just like gmx for the normal builds of GROMACS, mdrun_mpi needs to be found in your path. Typically that's convenient to do by installing a normal and the MPI-enabled mdrun-only build in the same place and sourcing the GMXRC from the former which ends up being suitable for the latter. Mark

Re: [gmx-users] implicit water simulation mpi

Hi, The last version where implicit solvent was known to work in parallel was 4.5.7 unfortunately. It wasn't maintained since then, and has been removed in very recent versions. Either use 4.5.7 or some other software, e.g. AMBER. Mark On Sun, 12 May 2019 at 01:33, Halima Mouhib wrote: > Hi,

Re: [gmx-users] EXTERNAL: Re: gromacs make check failure

Thanks for the clarification Paul. Cheers, Chris. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Paul bauer Sent: 21 May 2019 16:00 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] EXTERNAL: Re: gromacs make check failure

Re: [gmx-users] EXTERNAL: Re: gromacs make check failure

Hello Chris, in this case I think everything is fine with your build. As you can see from the MPI build log it is only the test harness complaining and nothing more. Happy simulations! Cheers Paul On 21/05/2019 16:00, Nelson Chris AWE wrote: Hi Paul, If I build without MPI, all tests

Re: [gmx-users] EXTERNAL: Re: gromacs make check failure

Hi Paul, If I build without MPI, all tests complete successfully. Cheers, Chris. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Paul bauer Sent: 20 May 2019 17:27 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] EXTERNAL:

Re: [gmx-users] implicit water simulation, Gromacs5.x, point decomposition

As far as I recall at most 2 ranks were supported; use OpenMP, I suggest. -- Szilárd On Sat, May 11, 2019 at 3:11 PM Halima Mouhib wrote: > Hi, > I have a question on how to run implicit water simulations using the > Gromacs5.x series. > Unfortunately, there is a problem with the domain

[gmx-users] How can I modify the speed of some atoms during each step？

Hi, I want to calculate the thermol conductivity of polymer. How can I modify the speed of some atoms during each step.Best regards,Ke Zhang

Re: [gmx-users] Regarding to find coordination number

Write a post processing code. It’s should be very easy to implement. You just need to choose an appropriate radius. Best, Prithwish Dr. Prithwish K Nandi, Ph.D. Computational Scientist Irish Centre for High-End Computing (ICHEC) - www.ichec.ie 7th Floor, The Tower, Trinity Technology &

Re: [gmx-users] control parameter on the Lennard-Jones interactions

Hi, This should be possible, e.g. with [pairs] on those particular atoms, or perhaps with tabulated non-bonded interactions (unfortunately only available with the group scheme) Mark On Thu, 16 May 2019 at 07:25, wrote: > > Dear gromacs members, > > I would ask you if in gromacs is possible to

Re: [gmx-users] Calculation of twist angle in gmx helix

Hi, On Tue, 21 May 2019 at 08:56, Sridip Parui wrote: > Dear Experts, > > When "gmx helix" is run, we obatin severals outputs, one of them helix > "twist angle". I do not know how the paramter is being calculated. I > manually calculated the angle between succesive C-Alpha atoms, between >

[gmx-users] Calculation of twist angle in gmx helix

Dear Experts, When "gmx helix" is run, we obatin severals outputs, one of them helix "twist angle". I do not know how the paramter is being calculated. I manually calculated the angle between succesive C-Alpha atoms, between succesive backbone carbonyl C atoms and also between successive backbone

[gmx-users] Regarding to find coordination number

Dear Experts, I performed a protein-water simulation in gromacs 2018.4. Now i am concentrating to find the coordination number of Oxygen atom of water molecule in whole system. Kindly help me to solve this problem. Thanks -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Calculation of twist angle in gmx helix

Dear Experts, When "gmx helix" is run, we obatin severals outputs, one of them helix "twist angle". I do not know how the paramter is being calculated. I manually calculated the angle between succesive C-Alpha atoms, between succesive backbone carbonyl C atoms and also between successive backbone