Re: [gmx-users] Multiple runs for same system

Or just direct me to the steps written anywhere On Saturday, 24 February 2018 3:51 PM, Dr. Seema Mishra wrote: Hi, Can anyone tell me the steps and commands for performing multiple runs of 50 ns for same protein-ligand system? Also the clustering for further

[gmx-users] definition electrical field in a special position

Hi all when I use E_z, it applies an electric field in the z direction, but I want to apply that in special thickness in the z direction, not in all length, is there any way to do it? Thanks in advance Regards Azadeh -- This email was Anti Virus checked by Security Gateway. -- Gromacs

Re: [gmx-users] Multiple runs for same system

Multiple runs are typically initiated simply by changing gen_seed when generating velocities at the outset of equilibration. As for clustering, you'll have to explain what you mean. Clustering ligand poses? Protein? What? Does a Google search for "GROMACS clustering" or the help information

Re: [gmx-users] Multiple runs for same system

On 2/25/18 6:07 PM, Dr. Seema Mishra wrote: Thanks Justin. Meaning I will simply set gen_seed as -1 instead of 173529. Right? However you want to do it, either by specifying a seed or letting grompp generate one. Some prefer the former for reproducibility, but given all the things that

Re: [gmx-users] Inconsistent Shifts

Iman, As I mentioned earlier, does the warning actually stop the simulation from running/completing? If not, then simply ignore it. One of the developers will need to chime in here about the error itself. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of

Re: [gmx-users] Multiple runs for same system

Thanks Justin. Meaning I will simply set gen_seed as -1 instead of 173529. Right? After this, how many runs will be performed? One? Then after the production run is finished, start it again with gen_seed=-1 for the second run? This is to be done for 3 independent runs for same protein-ligand

Re: [gmx-users] Inconsistent Shifts

On 2/25/18 6:27 PM, Dallas Warren wrote: Iman, As I mentioned earlier, does the warning actually stop the simulation from running/completing? If not, then simply ignore it. One of the developers will need to chime in here about the error itself. It would be helpful to know what exactly

Re: [gmx-users] definition electrical field in a special position

Hi, No that cannot be done Mark On Mon, Feb 26, 2018, 05:22 wrote: > Hi all > > when I use E_z, it applies an electric field in the z direction, but I > want to apply that in special thickness in the z direction, not in all > length, is there any way to do it? > > Thanks

[gmx-users] Inconsistent Shifts

Dear Dallas, I have tried the 2016.5 version of gromacs that it has the same warning about the inconsistent shifts. I don't know why it should arises as a warning and what is the problem. Is there another way to fix this warning? Sincerely Iman On Wed, Feb 21, 2018 at 11:26 AM, Iman Ahmadabadi

[gmx-users] walls with slab of water

Hi, I am trying to run a SLAB of water with a solute and I want to put a wall on the z axis edge. My problem is how to define *wall_atomtype *in the topology file or in the .itp I am using oplsaa.ff force field with SPC/E water. This is a section of the .mpd: Neighborsearching and short-range

Re: [gmx-users] energy minimization

Dear Justin In according to obtaining positive binding free energy using g_mmpbsa for my complex which has 2 phosphotyrosine residues and is simulated by charmm36 force field , I sent an email to g_mmpbsa mailing list and informed them to help me for solving my problem, but they replied me : "

Re: [gmx-users] Positive potential energy

Dear Justin, Thank you for your reply! In general, is it a good approach to first use steep algorithm for EM and then to further minimize do EM with cg algorithm, on the output structure? Could you please comment on my question about the mdp files and pbc as well? Actually, you mentioned here:

Re: [gmx-users] Positive potential energy

Dear Mark, Thank you for your reply. However, this is not clear for me yet since I read this in the tutorial from Justin: "There are two very important factors to evaluate and determine if EM was successful. The first is the potential energy (printed at the end of the EM process, even without

Re: [gmx-users] cut-off length error

On 2/23/18 1:03 PM, Mahmood Naderan wrote: Hi, I downloaded a water benchmark from gromacs web site and tried to run a sample. However it fails with a cut-off length error while there is no such parameter in topol.top mahmood@orca:~/gromacs-2018/bench/water-cut1.0_GMX50_bare/.65$ ls

Re: [gmx-users] Protein protein complex molecular dynamic simulation

On 2/24/18 7:06 AM, SHYANTANI MAITI wrote: Can molecular dynamic simulation be performed over protein-protein complexes using gromacs? Yes. This scenario is functionally no different than a single protein. pdb2gmx can write a topology for any multi-chain system, provided the input

Re: [gmx-users] Removal of Waters in Hydrophobic Core

On 2/22/18 1:33 PM, Smith, Iris wrote: Hi Justin, In a previous post (Nov 2016) between Chris Neal and Saint Rahman regarding removal of waters in hydrophobic core you mentioned the bilayer_seperator.pl script would be useful in conjunction with gmx traj. I am trying to determine the

Re: [gmx-users] Positive potential energy

On 2/25/18 10:15 AM, Mahsa wrote: Dear Justin, Thank you for your reply! In general, is it a good approach to first use steep algorithm for EM and then to further minimize do EM with cg algorithm, on the output structure? I usually don't find multiple steps of EM needed in most cases, but

Re: [gmx-users] Worse GROMACS performance with better specs?

BS”D Someone has pointed out to me that the “Silver” line is not meant for HPC. For HPC, you need to go with the “Gold” series, even if you don’t want 4 sockets. The difference presumably lies is the fact that the Gold has 2 FMA units, and the Silver series has 1. Harry On 20 Feb 2018,

[gmx-users] UNL residue error

Hello, I face an error in PDB file of cellulose to run GROMACS. I want to know what should I write in place of UNL residue. ATOM 1700 C UNL 1 29.680 -48.720 -19.563 0.00 -0.02 .177 C ATOM 1701 C UNL 1 13.970 -44.542 -17.378 0.00 -0.02 .177 C ATOM 1702 C UNL

Re: [gmx-users] UNL residue error

On 2/25/18 11:53 AM, Radhika Arora wrote: Hello, I face an error in PDB file of cellulose to run GROMACS. I want to know what should I write in place of UNL residue. ATOM 1700 C UNL 1 29.680 -48.720 -19.563 0.00 -0.02 .177 C ATOM 1701 C UNL 1 13.970 -44.542