[gmx-users] Topology for covalent bonds across periodic boundaries

Dear Gromacs users, I am trying to simulate an "infinite" protein chain by covalently bonding the last residue of my structure to the first residue across the periodic boundary. I have modified the topology file to include these bonded interactions and have specified "periodic-molecules=yes" in

Re: [gmx-users] 2019.2 build warnings

Okay, more interesting things are happening. At the end of 'make' I get a bunch of things like .. nbnxn_cuda.cu(373): warning: variable "dim_grid" was declared but never referenced -bash: syntax error near unexpected token `373' More errors during 'make check' right after "

[gmx-users] 2019.2 build warnings

Hi all, I am building the 2019.2 version, latest CUDA libs (older 2018 version works fine). While building, I am getting a ton of warnings as shown below, while the build does not terminate. Is this okay, or do we need to do anything at this point? Thanks, Alex

[gmx-users] Nonzero phase angles

​Dear all How can I translate the OPLS parameters to Ryckaert-Bellemans parameters (C0,C1,C2,C3,...) when the phase angles (f1,f2,f3,f4) are not zero. V=V0/2+V1/2(1-cos(Q-f1))+V2/2(1-cos(Q-f2))+V3/2(1-cos(Q-f3))+V4/2(1-cos(Q-f4)) Many thanks -- This email was Anti Virus checked by

[gmx-users] Generalized Energy Groups

Hi all, I'm currently trying to analyze the energy balance of a trajectory where I see various kinds of spatial partitioning of my molecules. I'd like to be able see a breakdown based on spatial group and atom type. However, I only know which molecules end up in which spatial region

[gmx-users] Nonzero phase angles

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Re: [gmx-users] -ignh command removes protonation site of interest

On 4/16/19 3:21 PM, Neena Susan Eappen wrote: I am using OPLS-AA force field and there are no parameters for protonated carbonyl for alanine residue. How do I go about this? What exactly are you trying to protonate? The oxygen in a peptide bond is not protonated. The C-terminus can be

Re: [gmx-users] -ignh command removes protonation site of interest

I am using OPLS-AA force field and there are no parameters for protonated carbonyl for alanine residue. How do I go about this? Thank you, Neena From: Neena Susan Eappen Sent: Monday, April 15, 2019 10:30 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject:

Re: [gmx-users] increase membrane dimensions

Sorry for the double post, but you could also try using CHARMM-GUI. http://www.charmm-gui.org/ That way you don't have to deal with implementing the Berger lipids into the gromos force field (note that CHARMM is all-atom while gromos is united-atom). I have only used it to make a pure lipid

Re: [gmx-users] increase membrane dimensions

Hi Emilio, > Is there a way of doing it using gromacs tools? Perhaps you can use gmx genconf? http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-genconf.html Have a look and see if it would work for you. I'm sure there are other ways that may be better, but this is the first that

[gmx-users] increase membrane dimensions

Dear Gromacs users, I want to simulate a protein embedded in a membrane made of POPC phospholipid. I have some experience with MD, but it is the first time that I am simulating a membrane protein. I am following the tutorial of KALP15 in DPPC membrane

Re: [gmx-users] Protein-Ligand interactions

Hi Use higher force constant and see what is happening On Tue 16 Apr, 2019, 6:14 PM RAHUL SURESH On Tue, Apr 16, 2019 at 1:57 PM Bratin Kumar Das < > 177cy500.bra...@nitk.edu.in> wrote: > > > Hi, > > The force you assigned for position restrain may not be enough to > hold > > the ligand

[gmx-users] Make check error

Hi, I met some errors when running make check after compiling the Gromacs 2019. Really appreciate it if anyone could help me. The Cmake info is listed as below: cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_SIMD=AVX2_256

Re: [gmx-users] Protein-Ligand interactions

On Tue, Apr 16, 2019 at 1:57 PM Bratin Kumar Das < 177cy500.bra...@nitk.edu.in> wrote: > Hi, > The force you assigned for position restrain may not be enough to hold > the ligand in the proper position. If u follow the gromacs tutorial ...the > simulation method is not wrong. > Thank you. I

Re: [gmx-users] GROMACS 2019.2 patch release available

Hello again, apologies for messing up the subject line, this is of course for the 2019.2 point release! Cheers Paul On 16/04/2019 13:41, Paul bauer wrote: Hi GROMACS users, The official release of GROMACS 2019.2 is available! This second patch release fixes several issues found since the

[gmx-users] GROMACS 2019.1 patch release available

Hi GROMACS users, The official release of GROMACS 2019.2 is available! This second patch release fixes several issues found since the last patch release of GROMACS 2019. We encourage all users of the 2019 series to update to 2019.2. Please see the link to the release notes below for more

Re: [gmx-users] calculation of pair wise interaction energy of residues

thank so much for your reply. Is there any loop which i can use to calculate all the residue pair wise interaction energy. So all the data can be handled. On Tue, Apr 16, 2019 at 2:29 PM Mark Abraham wrote: > Hi, > > You have to compute all the pairwise interactions if you want to compare >

[gmx-users] PCA with Gromacs

Dear Gmx users, I've been using Gromacs to perform Principal Component Analysis on my trajectories. 1- With gmx anaeig, we can plot a 2d projection of a trajectory on eigenvectors 1 and 2 (for example). I would like to know if there is a way to obtain the same plot but where the points are

Re: [gmx-users] -ignh command removes protonation site of interest

Or another way to keep the protonated state of residue is using -asp, -glu, -his ... and then you can manually assign the protonation state On Tue, Apr 16, 2019 at 1:06 AM Justin Lemkul wrote: > > > On 4/15/19 6:30 PM, Neena Susan Eappen wrote: > > Hello gromacs users, > > > > I started with a

Re: [gmx-users] standard error

Hi, I don't recall gmx analyze computing standard errors. But gmx analyze -h will report on what it does do :-) Does that help? Mark On Tue, 16 Apr 2019 at 08:58, Raag Saluja wrote: > Hi! > > What percent error is calculated as standard error by gmx analyze? 5%? > > Thank you in advance and

Re: [gmx-users] calculation of pair wise interaction energy of residues

Hi, You have to compute all the pairwise interactions if you want to compare all the pairwise interactions. But I'm deeply skeptical that you can learn anything from this anyway. The potential energy of typical force fields is not constructed to be decomposable, and such an analysis neglects the

Re: [gmx-users] Protein-Ligand interactions

Hi, The force you assigned for position restrain may not be enough to hold the ligand in the proper position. If u follow the gromacs tutorial ...the simulation method is not wrong. On Tue 16 Apr, 2019, 11:22 AM RAHUL SURESH Hi Users. > > A basic clarification on protein and small molecule

[gmx-users] standard error

Hi! What percent error is calculated as standard error by gmx analyze? 5%? Thank you in advance and regards, Raag -- 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