Re: [gmx-users] Ligand interaction

Dear md kashif, my protein energy is -1.5e+06 and now after docking with ligand it becomes -1.05e+06. what does it mean? is it is the energy of ligand_protein complex or simply the protein??? In docking generally the receptor is rigid, then why the receptor will change its energy ?? the

[gmx-users] Ligand interaction

Hello everyone please suggest me that is there any change in protein energy after docking the ligand to my energy minimized protein? my protein energy is -1.5e+06 and now after docking with ligand it becomes -1.05e+06. what does it mean? Thanks -- Gromacs Users mailing list * Please sea

Re: [gmx-users] lipid molecules are overlapping with proteinmolecule

hello justin, Energy minimization is not converging to Fmax in 2 steps in between shrinking steps. I tried it for 5 steps also, What can I do to resolve it..??? Regards, Padmani On Tue, Nov 11, 2014 at 6:08 PM, Justin Lemkul wrote: > [image: Boxbe]

Re: [gmx-users] New problem GROMACS 4.6.7 in Intel Cluster

On 11/11/14 8:59 PM, Agnivo Gosai wrote: Dear Users I thought that using MPI OFF commands in cmake will solve my problem. So I used the following command : -bash-4.1$ /work/gb_lab/agosai/GROMACS/cmake-2.8.11/bin/cmake .. -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_INSTALL_PREFIX=/work/gb_lab/agosai/gmx46

Re: [gmx-users] New problem GROMACS 4.6.7 in Intel Cluster

Dear Users I thought that using MPI OFF commands in cmake will solve my problem. So I used the following command : -bash-4.1$ /work/gb_lab/agosai/GROMACS/cmake-2.8.11/bin/cmake .. -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_INSTALL_PREFIX=/work/gb_lab/agosai/gmx465serial -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_CO

Re: [gmx-users] restarting of shifted potential, 4.6.7 bug?

Going from non-shift to shifted potential changes the energy. So I was not surprised by the sudden jump of energy between step 0 and step 10 for the previous simulation (npt14). But the jump near step 0 for the current simulation (npt15) is not right. This is an equilibration run. I have just up

Re: [gmx-users] restarting of shifted potential, 4.6.7 bug?

On Tue, Nov 11, 2014 at 3:38 PM, Johnny Lu wrote: > Hi. > > I ran 30ns NPT with Potential-shift-Verlet on both potentials, continuing > from a NPT without Potential-shift-Verlet. The energy dropped from -3e5 to > -4e5, which is fine. > > After that, I continue the 30ns NPT with the same mdp file,

Re: [gmx-users] Fwd: Re: Frequency dependent dielectric constant

Hello, I have managed to get dielectric constant. But it gives for very high frequency range. I am interested in low frequency range (typically less than 1000 GHz). How do I control range of frequency while calling g_dielectric function? Thank you. Bharat On Thu, Nov 6, 2014 at 4:44 PM, David va

Re: [gmx-users] restarting of shifted potential, 4.6.7 bug?

The system has 30k water and a protein with ~170 amino acid. Here are the PME tuning: npt14: DD step 4 load imb.: force 58.1% step 10: timed with pme grid 80 80 80, coulomb cutoff 1.000: 37.1 M-cycles step 20: timed with pme grid 64 64 64, coulomb cutoff 1.173: 32.6 M-cycles step 30: timed

Re: [gmx-users] restarting of shifted potential, 4.6.7 bug?

by the way, the machine has 4 Tesla K40m gpu, 32 xeon cpu with avx, and i ran: nohup ../../mdrun -deffnm npt15 -cpt 1 -cpnum & On Tue, Nov 11, 2014 at 9:38 AM, Johnny Lu wrote: > Hi. > > I ran 30ns NPT with Potential-shift-Verlet on both potentials, continuing > from a NPT without Potential-shif

[gmx-users] restarting of shifted potential, 4.6.7 bug?

Hi. I ran 30ns NPT with Potential-shift-Verlet on both potentials, continuing from a NPT without Potential-shift-Verlet. The energy dropped from -3e5 to -4e5, which is fine. After that, I continue the 30ns NPT with the same mdp file, except with a longer run time (300ns). The total energy was -4

Re: [gmx-users] GROMACS 5 - problem with LINCS with freeze groups

Hi Mark, Thank you for replay. I just checked this in Gromacs-4.6.7 and like you predicted I got same LINCS warning. I will fill bug report. Best, tomek On Tue, Nov 11, 2014 at 1:41 PM, Mark Abraham wrote: > Hi, > > You are using settings that trigger the group-scheme twin-range code. > There'

Re: [gmx-users] GROMACS 5 - problem with LINCS with freeze groups

Hi, You are using settings that trigger the group-scheme twin-range code. There's been a code bug there for a very long time, which we fixed after 4.6.5 (see http://redmine.gromacs.org/issues/1400. "Normal" usage such as in your .mdp file also tended to be broken when simulating water, which maske

Re: [gmx-users] Question about "Lysozyme in Water" tutorial by Dr. Lemkul

Two things to check: First try converting your trajectory to a pdb using trjconv instead of avogadro, as you can taken into account the perodic boundries. Second, ions can behave "oddly" in simulations due to hydration-effects; however, having them all cluster in a location is typically bad, as

[gmx-users] GROMACS 5 - problem with LINCS with freeze groups

Hi, I experience some strange behaviour and I wonder if this is a bug or I am doing something wrong. I am running test simulation to check freeze groups in new gromacs. And I am getting LINCS Warnings for atoms which should be frozen...: Step 0, time 0 (ps) LINCS WARNING relative constraint devi

Re: [gmx-users] Umbrella Sampling - Loop Motion

On 11/11/14 6:21 AM, Michael Carter wrote: Hi, I am setting up an umbrella sampling simulation to analyse the motion of a loop within my protein system. I have set it up so that the pull groups are: 1 – the loop (residues 208-14) 2 – the protein (protein) However, when doing this my confor

Re: [gmx-users] lipid molecules are overlapping with protein molecule

On 11/11/14 6:45 AM, Padmani Sandhu wrote: Hello all, I am trying to energy minimize a trimeric protein in DPPC bilayer but facing problem in reaching desired lipid per area using "inflategro.pl". After 5 or 6 steps of shrinking and energy minimization lipids molecules start interfering with

Re: [gmx-users] Very large Max Force [Energy minimisation] in water with ions

On 11/11/14 5:12 AM, Kester Wong wrote: Dear Justin and Erik, > Thank you for the feedback. I have also tried the following: > > i) separating OH- and Na+ ions > > ii) placing the ions much closer to water droplet > > iii) increase the spacing between each ions, i.

Re: [gmx-users] Error while running free energy simulation.

On 11/11/14 2:12 AM, vivek sharma wrote: Dear Users, I am trying to replicate the free energy tutorial by Dr Justin. In my attempt I have calculated the OPLS-AA FF parameters for my molecules of interest using acpype. I made the system in water and 1-octanol, While running the independent lambd

Re: [gmx-users] How much different run (with posre.itp) from no posre.itp?

On 11/11/14 12:30 AM, Batdorj Batsaikhan wrote: Dear gmx-users, I run 3 different conformation of a protein. I run 2 of them no posre.itp and another one has posre.itp. How much different these two run? Impossible to tell. You've got too many variables - different conformations, differen

[gmx-users] lipid molecules are overlapping with protein molecule

Hello all, I am trying to energy minimize a trimeric protein in DPPC bilayer but facing problem in reaching desired lipid per area using "inflategro.pl". After 5 or 6 steps of shrinking and energy minimization lipids molecules start interfering with protein. I tried to increase cutt-off, but that

[gmx-users] Umbrella Sampling - Loop Motion

Hi, I am setting up an umbrella sampling simulation to analyse the motion of a loop within my protein system. I have set it up so that the pull groups are: 1 – the loop (residues 208-14) 2 – the protein (protein) However, when doing this my conformations which I generate in the md_pull step a

Re: [gmx-users] Ligand is not in the same position as in PDB file

Hi, Did you consult the link I provided? ;-) Mark On Tue, Nov 11, 2014 at 11:18 AM, neha bharti wrote: > Thank you very much mark for your reply. > I merge the protein and ligand file before starting the molecular dynamics > simulation. > Then I start the MD run. > I don't how to post-process

Re: [gmx-users] Ligand is not in the same position as in PDB file

Thank you very much mark for your reply. I merge the protein and ligand file before starting the molecular dynamics simulation. Then I start the MD run. I don't how to post-process the output. can you please tell me how to perform it or is there any article or tutorial available for that. Thanks

Re: [gmx-users] Very large Max Force [Energy minimisation] in water with ions

Dear Justin and Erik, > Thank you for the feedback. I have also tried the following: > > i) separating OH- and Na+ ions > > ii) placing the ions much closer to water droplet > > iii) increase the spacing between each ions, i.e. using a larger box > > > Perhaps I should try having the ions

Re: [gmx-users] energy minimization of protein taken from PDB

Hi, That value may indicate that the ligand is not horribly out of place, because the total energy is negative. Showing a favourable binding interaction is a different matter, for which this is just the tiniest first step. Mark On Tue, Nov 11, 2014 at 9:04 AM, md kashif wrote: > Dear Dr. Justi

Re: [gmx-users] Ligand is not in the same position as in PDB file

Hi, Probably you are seeing normal behaviour in the presence of http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions. If you want to visualize the protein and ligand as a complex, you need to post-process the output accordingly. mdrun doesn't know that you plan to treat th

[gmx-users] Ligand is not in the same position as in PDB file

Hello All I am trying to perform MD for protein-ligand complex in popc lipid with charmm36 force field and also follow Justin A. Lemkul tutorial. I downloaded the pdb structure of protein and ligand complex and the separate the protein and ligand file and prepare the system. Finally I perform the

[gmx-users] energy minimization of protein taken from PDB

Dear Dr. Justin Lemkul Thanks for your kind suggestion, I have energy minimized my protein taken from PDB. It gives result as -1.5248922e+06. Taking the energy minimized protein generated in .gro file file and docking it with ligand and doining energy minimization again, it gives result as -1.0