Re: [gmx-users] QM/MM-ORCA Point Charge Correction Error (Zoe Chan)

Dear Gerrit, After trying a few different settings of .mdp, I found that "cutoff-scheme = Verlet" and "QMMMscheme = ONIOM" were causing the error. Would you have any idea how were these two settings linked to the generation of ".pc" file, and what would you suggest if I have to run under

Re: [gmx-users] Metal-Protein interactions

On 11/28/17 1:00 PM, RAHUL SURESH wrote: On Tue, 28 Nov 2017 at 7:14 PM, Justin Lemkul wrote: On 11/28/17 4:54 AM, RAHUL SURESH wrote: I am trying to simulate a metal-protein interaction using gromacs 2016 package and charmm36 ff. I have prepared the initial pdb by

Re: [gmx-users] GROMACS 2018 first beta released

First tests hints at ~10% better performance on Broadwell CPUs compared to 2016.4 on the ion_channel case we got from Erik L. This using the same compiler toolchain version. Will test more tomorrow :-) On 11/28/2017 07:09 PM, Mark Abraham wrote: > 2018 will look and work, and most importantly

Re: [gmx-users] Pressure through one direction

On Tue, Nov 28, 2017 at 12:25 PM, ali akgün wrote: > Hi, > > Can i generate mdp file for pressure through one direction system.For > example: > > Ref pressure: > > X direction:1.0 bar > Other direction: 0.0 bar > Yes, see the options here:

[gmx-users] GROMACS 2018 first beta released

Hi GROMACS users, The first beta release of GROMACS 2018 is available! (We know it's only 2017 right now, but by the time we make the real release it will be almost 2018, so that seems like a good idea!) We are making this available to you to get an early taste of how GROMACS 2018 will look and

Re: [gmx-users] Metal-Protein interactions

On Tue, 28 Nov 2017 at 7:14 PM, Justin Lemkul wrote: > > > On 11/28/17 4:54 AM, RAHUL SURESH wrote: > > I am trying to simulate a metal-protein interaction using gromacs 2016 > > package and charmm36 ff. > > I have prepared the initial pdb by performing an oniom calculations >

Re: [gmx-users] Not enough memory. Failed to realloc

Hi Yeah. I understood that.. thanks a lot for your patience On Tue, 28 Nov 2017 at 7:10 PM, Justin Lemkul wrote: > > > On 11/27/17 11:55 PM, RAHUL SURESH wrote: > > Dear Justin > > > > It worked. Actually by its own. I reconstructed the pdb and gave again. > > For the sake of

[gmx-users] Pressure through one direction

Hi, Can i generate mdp file for pressure through one direction system.For example: Ref pressure: X direction:1.0 bar Other direction: 0.0 bar Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] Pdb2gmx melts molecules due to bad distances

Thanks, but it doesn't work. Same problem. Gianmarco Bartalini Il 27 nov 2017 14:37, "Justin Lemkul" ha scritto: > > > On 11/27/17 6:04 AM, GIANMARCO BARTALINI wrote: > >> Hello guys, I produced a system "protein + lipid membrane" using the >> online >> tool CHARMM-GUI. Since

Re: [gmx-users] umbrella sampling

On Mon, Nov 27, 2017 at 2:30 AM, rose rahmani wrote: > > > On Mon, Nov 27, 2017 at 1:55 AM, Alex wrote: > >> Hi, >> >> The answer is clearly in the error, just read it please: >> 2.848793 > 0.49 * (4/2) where 4 is the box length. >> >>> But i

Re: [gmx-users] Umbrella sampling

On 11/28/17 10:00 AM, rose rahmani wrote: Would "pull_geometry=periodic-distance" be another solution for it? No. That affects how the reaction coordinate distance is calculated, not the PBC treatment, which is intrinsic to any simulation using PBC. -Justin On Tue, Nov 28, 2017 at 5:11

Re: [gmx-users] Umbrella sampling

Would "pull_geometry=periodic-distance" be another solution for it? On Tue, Nov 28, 2017 at 5:11 PM, Justin Lemkul wrote: > > > On 11/28/17 12:23 AM, rose rahmani wrote: > >> Hello; >> >> I took 2000 configuration from trajconv. Amino acid is in its normal shape >> till almost

Re: [gmx-users] Metal-Protein interactions

On 11/28/17 4:54 AM, RAHUL SURESH wrote: I am trying to simulate a metal-protein interaction using gromacs 2016 package and charmm36 ff. I have prepared the initial pdb by performing an oniom calculations between protein and metal (at various positions) using gaussian 09 and chose the

Re: [gmx-users] Umbrella sampling

On 11/28/17 12:23 AM, rose rahmani wrote: Hello; I took 2000 configuration from trajconv. Amino acid is in its normal shape till almost conf1000.gro(and a little more). But in for example conf1300.gro amino acid was disintegrated. What does it mean? Would you please help me? Bonds can't

Re: [gmx-users] Not enough memory. Failed to realloc

On 11/27/17 11:55 PM, RAHUL SURESH wrote: Dear Justin It worked. Actually by its own. I reconstructed the pdb and gave again. For the sake of completeness, the original problem was indeed due to a massive box size, which was probably just incorrectly set. You had a 92-nm y-box vector and

[gmx-users] Metal-Protein interactions

I am trying to simulate a metal-protein interaction using gromacs 2016 package and charmm36 ff. I have prepared the initial pdb by performing an oniom calculations between protein and metal (at various positions) using gaussian 09 and chose the structure with maximum binding energy. The metal ion