Re: [gmx-users] virtual site connected to dummy massive site

Hi, Your systems have different available degrees of freedom, so they sample difference spaces. The energies you observe reflect that difference. Mark On Mon, 20 Nov 2017 18:18 Faezeh Pousaneh wrote: > Hi, > > I have a system containing of a virtual site of carbon

Re: [gmx-users] Regarding calculating the water orientation profile

Hi, "Coming closer" implies you care about distance, but your original question was about orientation. So it's unclear what you want. Mark On Thu, 23 Nov 2017 16:50 Dilip H N wrote: > I want to calculate whether the water molecules are coming closer towards > the

Re: [gmx-users] Regarding calculating the water orientation profile

Hi Dilip, Here is what you can do. In my guess, you are trying to calculate the preferential binding affinity of water for N/C terminal domain of your protein. You can look up for papers that contain Kirkwood-Buff integrals and preferential binding coefficients. It basically works in the

Re: [gmx-users] Regarding calculating the water orientation profile

Hi Joao Sir, Yes, that was me, who had asked the questions some time ago, but i had no success in this. Sent with Mailtrack

Re: [gmx-users] how to checkpoint per steps

On 11/23/17 10:02 PM, Du, Yu wrote: Dear GMX Users, In GMX, I can't checkpoint per some MD steps but only checkpoint per wall time period, right? Right. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of

[gmx-users] how to checkpoint per steps

Dear GMX Users, In GMX, I can't checkpoint per some MD steps but only checkpoint per wall time period, right? -- Du, Yu PhD Student, Shanghai Institute of Organic Chemistry 345 Ling Ling Rd., Shanghai, China. Zip: 200032, Tel: (86) 021 5492 5275 -- Gromacs Users mailing list * Please

Re: [gmx-users] Does RMSD only consider the "relative" coordinate changes for the selected group?

On 11/23/17 11:20 AM, ZHANG Cheng wrote: Dear Gromacs, When I calculate the RMSD for the whole protein, I got values mostly from 0.2-0.5 nm. However, when I only calculate for a particular residue (using an index file), the scale is mostly only 0.01-0.02 nm, even for a residue on the loop.

Re: [gmx-users] THE max number of atoms in gromacs?

Amazing! Thank you so much! On Fri, Nov 24, 2017 at 5:22 AM, João Henriques < joao.m.a.henriq...@gmail.com> wrote: > Hi, > > The PDB format is fixed, so it's not really a gromacs problem *per se*. > Take a look at this >

Re: [gmx-users] THE max number of atoms in gromacs?

Hi, The PDB format is fixed, so it's not really a gromacs problem *per se*. Take a look at this : "A model cannot have more than 99,999 atoms. Where the entry does not contain an ensemble of models, then the entry

[gmx-users] THE max number of atoms in gromacs?

Hello gmx-users: I build a large system with more than 10,000 atoms, however I cannot write info to pdb file correctly. The pdb file format in gromacs specify 5 positions for atom-id, and it will cause problem if not. Since I have to use rtp file and "pdb2gmx" command to generate conf.gro and

Re: [gmx-users] Regarding calculating the water orientation profile

Wait, now I remember, you even approached me in a private message and we exchanged quite a few emails. Did you try any of my suggestions? No success? J On Thu, Nov 23, 2017 at 7:36 PM, João Henriques < joao.m.a.henriq...@gmail.com> wrote: > Hi, > > I clearly remember replying to something

Re: [gmx-users] Regarding calculating the water orientation profile

Hi, I clearly remember replying to something similar sometime ago, and I'm almost sure the post was yours. It may be a good idea to rummage through the mailing list, because I'm pretty sure this type of analysis has been discussed here more than once. Cheers, J On Thu, Nov 23, 2017 at 4:41 PM,

[gmx-users] Build thin film.

I have a pdb file can i build thin film ? -- 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

[gmx-users] Does RMSD only consider the "relative" coordinate changes for the selected group?

Dear Gromacs, When I calculate the RMSD for the whole protein, I got values mostly from 0.2-0.5 nm. However, when I only calculate for a particular residue (using an index file), the scale is mostly only 0.01-0.02 nm, even for a residue on the loop. My understanding is: when doing the RMSD,

Re: [gmx-users] Regarding calculating the water orientation profile

I want to calculate whether the water molecules are coming closer towards the N-terminal or towards the C-terminal of the amino-acid throughout the simualtion. And hence it can shed some light on the Hydrogen bond dynamicshopefully... Thank you Sent with Mailtrack

Re: [gmx-users] Topology file of molecule

On 11/23/17 7:51 AM, Magnus Lundborg wrote: Dear Krzysztof, I wouldn't be too worried about the fact that GAFF parameters have been used for proper and improper torsion angles. It happens quite a lot with the OPLS-AA forcefield. But as always, it is good to verify that the topology behaves

Re: [gmx-users] Topology file of molecule

Dear Krzysztof, I wouldn't be too worried about the fact that GAFF parameters have been used for proper and improper torsion angles. It happens quite a lot with the OPLS-AA forcefield. But as always, it is good to verify that the topology behaves as expected. Unfortunately there is no

Re: [gmx-users] Restarting simulation from not last checkpoint but previous to last check point

Hi, Yes. Back up your files, then start using -cpi state_prev.cpt as part of your mdrun command. Mark On Thu, 23 Nov 2017 12:13 atb files wrote: > > > > > Hi Experts,I am restarting the simulation using command gmx > mdrun -deffnm name -v -c -s topol.tpr -cpi

Re: [gmx-users] Regarding calculating the water orientation profile

Hi, It sounds like to need to be more clear about what you want to calculate before you can sensibly find a tool to do it. You should be able to write down the equation for what you want to compute as your observation long before you run a simulation, or how will you know what data to collect?

Re: [gmx-users] how to set hetrodimer for MD Simulation

Dear Rana, a) We are not (necessarily) Amber users. This is a gromacs mailing list. b) If the separate structures are correctly positioned relative to each other, you basically just need to cut-and-paste the ATOM records from one pdb file into the other one. Kind regards, Erik

[gmx-users] Restarting simulation from not last checkpoint but previous to last check point

Hi Experts,I am restarting the simulation using command gmx mdrun -deffnm name -v -c -s topol.tpr -cpi name.cpt -appendGromacs giving error that your checkpoint file is empty/currupted, it happened due to disk space. Can I set checkpoint not latest but the one

[gmx-users] Topology file of molecule

Dear Gromacs Users, I would like to perform a simulation of adsorption of 3,4-Dihydroxybenzoic acid (34DHBA) on silica surface using the OPLS-AA forcefield. I created topology files for the silica surface based on the information found in papers describing simulations of quartz (Wensink 2000 -