Re: [gmx-users] What is the equivalent command for insert-molecules in Gromacs 3.3.1?

At that time the command was "genbox" I think, that you could use to insert multiple molecules. 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] What is the equivalent command for insert-molecules in Gromacs 3.3.1?

Hi, The file formats read by grompp haven't changed, so you can prepare your system with a modern version of GROMACS, and call grompp for that old one. But I have a hard time imagining a method that was implemented in 3.3.1 still being useful. Even an enhanced sampling method would have to

Re: [gmx-users] RMSD analysis and stability

On 9/15/19 7:27 AM, Bratin Kumar Das wrote: You can see the radius of gyration, number of hydrogen bond, native contact etc for assessing the stability Overall, "stability" implies persistence of important interactions (really it implies knowledge of free energy of the system, but

Re: [gmx-users] Batch mode error in GROMACS version 2019.2

That makes sense. Thanks, a lot. On Sun, Sep 15, 2019 at 4:53 PM Mark Abraham wrote: > Hi, > > I can imagine some MPI setups would control whether and how the shell > streams used in such redirections are passed through, so the fact that gmx > works and gmx_mpi doesn't seems consistent. Use gmx

Re: [gmx-users] RMSD analysis and stability

You can see the radius of gyration, number of hydrogen bond, native contact etc for assessing the stability On Sun 15 Sep, 2019, 4:32 PM Quin K, wrote: > Thank you! > What else should I be looking for? > [image: mailcastr branding] Sent with Mailcastr > < >

Re: [gmx-users] Batch mode error in GROMACS version 2019.2

Hi, I can imagine some MPI setups would control whether and how the shell streams used in such redirections are passed through, so the fact that gmx works and gmx_mpi doesn't seems consistent. Use gmx if you need scripting. You only need the MPI build for running mdrun, so you'll have a good time

Re: [gmx-users] RMSD analysis and stability

Thank you! What else should I be looking for? [image: mailcastr branding] Sent with Mailcastr On Sun, Sep 15, 2019 at 4:16 PM Justin Lemkul wrote: > > > On 9/15/19 5:30 AM, Quin K wrote: > > Hi everyone!

Re: [gmx-users] Amber 14SB force-field problem with residue HID

On 9/12/19 7:08 PM, Kevin wrote: Dear Users, I have encountered a problem with the Amber force-field downloaded from http://www.gromacs.org/Downloads/User_contributions/Force_fields. Whenever I feed this forcefield to pdb2gmx and get a residue HID for protein topology, it will cause error

Re: [gmx-users] What is the equivalent command for insert-molecules in Gromacs 3.3.1?

On 9/14/19 4:59 PM, ZHANG Cheng wrote: Dear All, Due to a software that is only compatible to Version 3.3.1, I have to use that to prepare the simulation box. I was told "command not found?? when using the insert-molecules. So what should I do to put multiple molecules in a box? Use a

Re: [gmx-users] RMSD analysis and stability

On 9/15/19 5:30 AM, Quin K wrote: Hi everyone! I have done a MD simulation for a protein structure at 310K (100ns) this is the RMSD at around 65 ns kindly comment on the stability. Will I have to rerun the MD? Kindly let me know how to decide stability by analyzing RMSD. RMSD alone is

Re: [gmx-users] Regarding obtaining potential energy using, energy groups

On 9/15/19 6:09 AM, Nirali Desai wrote: Hello, Thank you so much. I have taken two groups at a time only and calculated the energies (Defining using index). My question is if I have done it for the two groups 1. AB 2. C. Does that energy also include the intramolecular interaction energy

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 185, Issue 50

> > Hello, > Thank you so much. I have taken two groups at a time only and calculated the energies (Defining using index). My question is if I have done it for the two groups 1. AB 2. C. Does that energy also include the intramolecular interaction energy of A & B?. Please guide me on this.

[gmx-users] RMSD analysis and stability

Hi everyone! I have done a MD simulation for a protein structure at 310K (100ns) this is the RMSD at around 65 ns kindly comment on the stability. Will I have to rerun the MD? Kindly let me know how to decide stability by analyzing RMSD. For backbone

Re: [gmx-users] Regarding obtaining potential energy using energy groups

Den 2019-09-14 kl. 23:32, skrev Najamuddin Memon: It depends on interaction of proteins i.e A interacts with B A both interact with C Only A or only B interacts with C In 2nd option you can make one group (A) and 2nd group as C Note that this only tells you about non-bonded interaction at