Re: [gmx-users] mismatch sol.gro/topol.gro

I understand that transferring a system organized for namd-charmm36 ro gromacs-charmm36 involves blind usage of transformation tools that are not from gromacs. In the specific case, the tool became confused by the ligand having a side chain with hyphened atom numbering, should the mismatch between

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

http://www.gromacs.org/Documentation/Errors?highlight=periodicity#System_has_non-zero_total_charge On Fri, 30 Nov. 2018, 5:14 am Ali Khodayari < ali.khoday...@student.kuleuven.be wrote: > Dear gmx community, > > > > I am getting a note before performing the energy minimization step, from >

[gmx-users] TIP3P water

Hi all, We normally use TIP4P water for our work, but need to test TIP3P. Everything is scripted, so I did minimal changes that hopefully follow http://www.gromacs.org/Documentation/How-tos/TIP3P_coordinate_file In the topology, we are including tip3p.itp In the run script, we are solvating with

[gmx-users] Frozen groups lead to a high energy

Dear gromacs users I'm simulation a hydrocarbon and water mixture placed on a slab of metal. The metal surface is frozen in the z-direction. Energy minimization works with no errors but I see the potential energy is too high as below. Steepest Descents converged to machine precision in 1754

[gmx-users] non-zero total charge

Dear gmx community, I am getting a note before performing the energy minimization step, from grompp that "System has non-zero charge: -0.001135". The system is a crystalline cellulose, built in Amber, using GLYCAM06 force field and the topology and coordinate files have been converted to

Re: [gmx-users] Running Grompp in reverse and backing up MD data

Hi, Hopefully early in 2019 we will get to the point where the mdp inputs are expressed as key-value data structures, perhaps in JSON. Once we do that, that aspect of the .tpr no longer needs to be binary, and dumping it is trivial. Mark On Thu, Nov 29, 2018 at 5:17 PM Thomas Piggot wrote: >

Re: [gmx-users] Running Grompp in reverse and backing up MD data

Good to know, thanks! Tom On 29/11/2018 16:08, Paul bauer wrote: Hello, just a warning concerning the last message: The mdp from gmx dump -om will not be the complete representation of your tpr, and you will not be able to regenerate the tpr from this mdp file! I have been working on a

Re: [gmx-users] Running Grompp in reverse and backing up MD data

Hello, just a warning concerning the last message: The mdp from gmx dump -om will not be the complete representation of your tpr, and you will not be able to regenerate the tpr from this mdp file! I have been working on a variant that would make this possible, but so far have not managed it.

Re: [gmx-users] Running Grompp in reverse and backing up MD data

You can get an mdp from a tpr using gmx dump -om Cheers Tom On 29/11/2018 14:58, Peter Kroon wrote: Hi all, thanks for all the feedback. @Milan: I've made a tally of diskspace used per filetype in our lab. In general people here don't save trr files at all (too expensive), yet still out of

Re: [gmx-users] Running Grompp in reverse and backing up MD data

Hi all, thanks for all the feedback. @Milan: I've made a tally of diskspace used per filetype in our lab. In general people here don't save trr files at all (too expensive), yet still out of 125TB total, 65% is made up of xtc files, and 10% is trr files (followed by gro and xvg at 2.5% each).

Re: [gmx-users] Running Grompp in reverse and backing up MD data

Hi, Yes, that's useful output, though strictly some mdp settings (like constraints and gen-vel) are consumed by grompp and thus not reported there. Mark On Thu, Nov 29, 2018 at 3:16 PM Justin Lemkul wrote: > > > On 11/29/18 6:43 AM, Peter Kroon wrote: > > Hi Mark, > > > > thanks for the rapid

Re: [gmx-users] Stacking

Thanks for your reply sir. It's very useful input for me. On Thu 29 Nov, 2018, 7:48 PM Justin Lemkul > > On 11/27/18 10:53 PM, Bratin Kumar Das wrote: > > Dear all, > > I have one pdb structure obtained from the solution NMR. > It is > > a peptide fragment. I want to stack it for

Re: [gmx-users] Parameterizing N-terminal capping

On 11/27/18 3:43 PM, Raji wrote: Hi Thank you for your reply. To parameterize the dihedrals, OSL-CL-NH1-H, OSL-CL-NH1-CT1, NH1-CL-OSL-CTL2 (OSL,CL, CTL2 from carboxy benzyl capping and NH1, H, CT1 from peptide backbone) How to segment the molecule with peptide backbone? The model compound

Re: [gmx-users] Stacking

On 11/27/18 10:53 PM, Bratin Kumar Das wrote: Dear all, I have one pdb structure obtained from the solution NMR. It is a peptide fragment. I want to stack it for studying aggression studies. How I can do that. Any suggestions are highly appreciable. Use editconf to manipulate

Re: [gmx-users] Running Grompp in reverse and backing up MD data

Hi, On Thu, Nov 29, 2018 at 3:05 PM melichercik wrote: > Hi Peter, > may be the gmx dump -s *.tpr can help you a little with extracting > starting data from .tpr file. You would get all interactions, positions > and velocities of all atoms with their types, etc., but the data about > aminoacid

Re: [gmx-users] Running Grompp in reverse and backing up MD data

On 11/29/18 6:43 AM, Peter Kroon wrote: Hi Mark, thanks for the rapid reply! Hmmn. It doesn't have to be exactly matching input. An equivalent to e.g. mdout.mdp produced by grompp would already be good enough for my All of the input .mdp settings are also written to the header of the

Re: [gmx-users] Running Grompp in reverse and backing up MD data

Hi, On Thu, Nov 29, 2018 at 12:43 PM Peter Kroon wrote: > Hi Mark, > > thanks for the rapid reply! > > Hmmn. It doesn't have to be exactly matching input. An equivalent to > e.g. mdout.mdp produced by grompp would already be good enough for my > purposes. The same goes for a top file containing

Re: [gmx-users] Running Grompp in reverse and backing up MD data

Hi Peter, may be the gmx dump -s *.tpr can help you a little with extracting starting data from .tpr file. You would get all interactions, positions and velocities of all atoms with their types, etc., but the data about aminoacid sequence (well, all more complex informations that those

[gmx-users] Open position: Join the Gromacs team to work on training, workflows, and industry collaborations

Hi, As part of the BioExcel Center-of-Excellence for Biomolecular Simulation, we have a new opening for somebody interested in joining the Gromacs team in Stockholm to work specifically on training, use cases, creating high-throughput workflows for simulations, and not least develop industrial

Re: [gmx-users] Running Grompp in reverse and backing up MD data

Hi Mark, thanks for the rapid reply! Hmmn. It doesn't have to be exactly matching input. An equivalent to e.g. mdout.mdp produced by grompp would already be good enough for my purposes. The same goes for a top file containing only the interactions relevant to the system. Peter On 29-11-18

Re: [gmx-users] How to fix graphite layers?

Your reply is very helpful to me. Thank you Alex! > -Original Messages- > From: Alex > Sent Time: 2018-11-29 16:59:20 (Thursday) > To: gmx-us...@gromacs.org > Cc: > Subject: Re: [gmx-users] Re: Re: Re: How to fix graphite layers? > > > > My current plan is to divide the two atoms into

Re: [gmx-users] Running Grompp in reverse and backing up MD data

Hi, Unfortunately there is no way to generate matching inputs to grompp from a .tpr file. In the longer term, we want that to be possible, but it will require a total rework of how users specify inputs, and that's a large effort! Mark On Thu, Nov 29, 2018 at 11:27 AM Peter Kroon wrote: > Hi

[gmx-users] Running Grompp in reverse and backing up MD data

Hi all, In the lab we're thinking about backup solutions for MD data (and in particular gromacs produced data). Since trajectories tend to be large we quickly decided that backing up the results of simulations is a waste of disk space. Instead, we'll probably go for backing up the TPR files.

Re: [gmx-users] [CASS SPAM]Re: [CASS SPAM]Re: [CASS SPAM]Re: How to fix graphite layers?

My current plan is to divide the two atoms into two groups and set the peripheral atoms to the frozen group in mdp file. I am not sure what the interaction between the frozen and active groups is. If I need to generate top files for each of these two groups, how should I tell the 'hot

Re: [gmx-users] [CASS SPAM]Re: [CASS SPAM]Re: [CASS SPAM]Re: How to fix graphite layers?

Dear Alex: Thank you very much for your reply. I am sorry that I did not make my research background clear at first. I want to explore the nature of the methane in organic pores in the formations thousands meter underground. In order to simplify the problem, graphite is used as a material for

Re: [gmx-users] [CASS SPAM]Re: [CASS SPAM]Re: How to fix graphite layers?

I re-checked the initial configuration： The interlayer distance is 0.34nm， which is consistent with other data descriptions. That is the interlayer distance that corresponds to the experimental data for HOPG graphite. Whether it is compatible with the LJ parameters of your carbons is a