[gmx-users] Amber14sb cutoff

this paper "ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB” to find the cutoffs, but sadly, I couldn’t find them. I greatly appreciate your help. Thanks, Thanh Le -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Su

[gmx-users] Run time for energy minimization, nvt, and npt equilibration

since I read in the literature gromacs would use all the available cores to run if I dont specify the number of cores. Thanks, Thanh Le -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post?

[gmx-users] Run time for energy minimization, nvt, and npt equilibration

ocumentation/Acceleration_and_parallelization >Consult with your sysadmin for best performance on whatever hardware you have. I will talk to my sysadmin about it. Thanks, Thanh Le -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_List

[gmx-users] Running Gromacs in parallel

ssible cores and nodes? Thanks, Thanh Le -- 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

[gmx-users] Any advice on finding the binding energy from RNA Protein interaction?

substitution in the peptide. If there are other ways to do this, please advice me. Thanks, Thanh Le -- 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/Su

[gmx-users] Atoms in the .top are not numbered consecutively from 1

Hi Gandhi, My name is Thanh Le, a graduate student in chemistry. Currently, I am using gromacs to do a dynamics simulation for my RNA-protein complex. I saw you posted a question titled “Atoms in the .top are not numbered consecutively from 1” on gromacs forum. I know it has been 4 years since

Re: [gmx-users] md with multiple ligands

> On Jun 30, 2016, at 3:48 PM, Thanh Le wrote: > > My name is Thanh Le, a graduate student in chemistry. Currently, I am using > gromacs to do a dynamics simulation for my RNA-protein complex. I saw you > posted a question titled “Atoms in the .top are not numbered consecutivel

[gmx-users] MBAR bootstrap

point me to the correct direction to implement bootstrap? Or any advice on how to analyze MBAR? Thanks, Thanh Le -- 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.gromac

[gmx-users] Question about gmx bar

Hi everyone, I just finished running 2 sets of simulations (ligand in water and RNA+ligand in water) for my system to learn about its binding energy. Using the parameter for BAR method, I ran 20 simulations for ligand in water and 30 simulations for RNA+ligand in water with different lambda sta

[gmx-users] Question about gmx bar

another way to do it? Is there a paper I can read to get more details about the subject? Thanks, Thanh Le On 2/27/18 4:13 PM, Thanh Le wrote: > Hi everyone, > I just finished running 2 sets of simulations (ligand in water and RNA+ligand > in water) for my system to learn about it

[gmx-users] Protein atomic charges modeling question

Is there a program or algorithm for calculating atomic charges in protein R group amino acid residues in various conditions (ie ligand binding partners, solutions of various pH, hydrophobic pockets, etc)? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Suppo

[gmx-users] Running MD jobs using slurm on multiple nodes

, Thanh Le -- 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/lis

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 158, Issue 186

Hi Mr. Abraham. My system is quite small, only about 8000 atoms. I have run this system for 100 ns, which took roughly about 2 days. Hence, a run of 1 microsecond would take about 20 days. I am trying to shorten it down to 2 days by using more than 1 node. Thanks, Thanh Le > On Jun 29, 2017,

[gmx-users] Problems running on multiple nodes

ime to run. Any advice is greatly appreciated. Thanks, Thanh Le -- 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