Re: [gmx-users] REMD mdrun_mpi error

Hi Mark, I tried to run an individual tpr file and it crashed: Double sids (0, 1) for atom 26 Double sids (0, 1) for atom 27 Double sids (0, 1) for atom 28 Double sids (0, 1) for atom 29 Double sids (0, 1) for atom 30 Double sids (0, 1) for atom 31 Double sids (0, 1) for atom 32 Double sids (0,

[gmx-users] constraint pull code / gromacs 5.0.4

Dear gromacs users, I'm using the pull code to evaluate the Potential of Mean Forces between two nanoparticles(NPs) of Radius = 1nm. Specifically, in order to create the configurations (i.e.the 2 NPs at different centr of mass distance) I used the constraint pull code. Then for each

Re: [gmx-users] installation errors

Thanks Mark! I could install it at last. I installed it in a desired directory not in root, used --enable-shared and --disable-float. that was the only way it was installed! and I should say I tried from all versions 5 to 4 and finally the one without errors was 4.5.5! (with fftw-3.3.4) I have 2

Re: [gmx-users] Does Gromacs take advantage of ECC memory?

Dear Andrew, ECC is Error Correction Code for the memory and is not related to you application. For a single-user workstation, you generally don't need the ECC. It is more important in servers. Not every motherboard supports ECC and most desktop motherboards do not, so if you do get it, you

Re: [gmx-users] Protein-DNA simulation LINKS error

On 6/23/15 7:13 AM, Timofey Tyugashev wrote: I'm trying a few simulations of a enzyme-DNA complex and while in short timeframes (up to 5ns) the behaviour looks quite normal, a 10ns simulation crashes with numerous LINCS warnings. Maybe there are some errors in mdp configuration file? To mine

Re: [gmx-users] Does Gromacs take advantage of ECC memory?

On 23/06/15 20:33, Peter Stern wrote: Dear Andrew, ECC is Error Correction Code for the memory and is not related to you application. For a single-user workstation, you generally don't need the ECC. It is more important in servers. Not every motherboard supports ECC and most desktop

Re: [gmx-users] constraint pull code / gromacs 5.0.4

On 6/23/15 4:28 PM, Alex wrote: It's dangerous to make broad generalizations like constraints should be deprecated. Sometimes constraints are not appropriate (materials, crystals, etc). But for the vast majority of biomolecular simulations, we really don't care about different vibrational

Re: [gmx-users] gas phase force field

On 6/23/15 12:45 AM, Swapnil Kate wrote: hello, Thanks for yours valuable comments, So Which force fields do you people recommend to simulate gas phase systems?Can we simulate gas and liquid mixtures in one go? What does your evaluation of the literature tell you? Which force fields do

Re: [gmx-users] constraint pull code / gromacs 5.0.4

On 6/23/15 2:10 PM, Alex wrote: The pulling rate, as it appears in your mdp, is actually zero. That aside, ...which is correct if one is sampling independent windows and collecting the forces to reconstruct the PMF. What is atypical is the application of a constraint rather than a

Re: [gmx-users] gas phase force field

OPLS is a good choice to start with On Tue, Jun 23, 2015 at 1:45 AM, Swapnil Kate swapnilk...@rocketmail.com wrote: hello, Thanks for yours valuable comments, So Which force fields do you people recommend to simulate gas phase systems? Can we simulate gas and liquid mixtures in one go?

Re: [gmx-users] Protein-DNA simulation LINKS error

I have ordinary DNA and an oxoguanine site? What actions should I take to correct these vsite parameters? Message: 1 Date: Tue, 23 Jun 2015 22:24:20 + From: Erik Marklund erik.markl...@chem.ox.ac.uk To: gmx-us...@gromacs.org gmx-us...@gromacs.org Subject: Re: [gmx-users] Protein-DNA

[gmx-users] About g_helix

Hello, Is it possible to calculate the average twist, turn, rise etc of a DNA molecule using g_helix? I am trying to show how the native conformation of the nucleic acid gets distorted on interacting with some carbon based nanoparticles. if yes, can anyone help me understanding

Re: [gmx-users] GMX_LARGEFILES looks ignored in cmake of gromacs-5.0.5

Hi, On Tue, Jun 23, 2015 at 10:07 AM Makoto Yoneya makoto-yon...@aist.go.jp wrote: Dear GROMACS users: I found that GMX_LARGEFILES looks ignored in cmake of gromacs-5.0.5 (e.g. cmake -DGMX_LARGEFILES=OFF bra-bra). At the end of cmake, it says CMake Warning: Manually-specified variables

[gmx-users] GMX_LARGEFILES looks ignored in cmake of gromacs-5.0.5

Dear GROMACS users: I found that GMX_LARGEFILES looks ignored in cmake of gromacs-5.0.5 (e.g. cmake -DGMX_LARGEFILES=OFF bra-bra). At the end of cmake, it says CMake Warning: Manually-specified variables were not used by the project: GMX_LARGEFILES. Although, there are lines,

Re: [gmx-users] GMX_LARGEFILES looks ignored in cmake of gromacs-5.0.5

Hi, yes the variable is ignored. Because with GROMACS 5 large file support is required. Thus if the variable is set to false it also prints a fatal error. It was never a variable which was suppose to be set by the user. Why do you ask? What do you try to achieve? Roland On Tue, Jun 23, 2015 at

[gmx-users] calculation of total no of hydrogen bond present in the system

Dear All Gromacs users I am try to calculate total no of hydrogen bond present in a system. For that I am using gromacs 5.0.2 (gmx hbond ). The problem is that I am unable to specify donor and acceptor during input. I am using Amber coordinate and topology file that is converted to gromacs

[gmx-users] (no subject)

Dear All Gromacs users I am try to calculate total no of hydrogen bond present in a system. For that I am using gromacs 5.0.2 (gmx hbond ). The problem is that I am unable to specify donor and acceptor during input. I am using Amber coordinate and topology file that is converted to gromacs

Re: [gmx-users] calculation of total no of hydrogen bond present in the system

Dear Rahman, The donors are not the hydrogens, but the oxygens to which they are bonded. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow Fulford JRF, Somerville College Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road

[gmx-users] About g_helix

Hello, Is it possible to calculate the average twist, turn, rise etc of a DNA molecule using g_helix? I am trying to show how the native conformation of the nucleic acid gets distorted on interacting with some carbon based nanoparticles. if yes, can anyone help me understanding

Re: [gmx-users] REMD mdrun_mpi error

Hi, Do your individual replica .tpr files run correctly on their own? Mark On Mon, Jun 22, 2015 at 3:35 PM Nawel Mele nawel.m...@gmail.com wrote: Dear gromacs users, I am trying to simulate a ligand using REMD method in explicit solvent with the charmm force field. When I try to

[gmx-users] Umbrella Sampling problem

Dear all, I follow the Umbrella Sampling tutorial, and have some problems:1. pdb2gmx with -ter have warning TYR-1 missiong H2. grompp -f npt_umbrella.mdp have 1 warning, but I avoid it.3. Gromacs 4.6.7 and gromacs 5.0.4 have same result: energy minimum is 24.8 kcal mol-1So, what happed in my

[gmx-users] REMD with different structures

Hi I am trying to do NVT REMD simulations with gromacs. I have 60 replicas and each of them have different starting structure . The starting structures have same number of atoms but slightly different volume and pressure. I was able to run these simulations but I want to know if having

Re: [gmx-users] Protein-DNA simulation LINKS error

The vsite parameters are not complete for DNA/RNA. Perhaps you have faster oscillations in your system than you intended to have. Erik On 23 Jun 2015, at 21:15, Justin Lemkul jalem...@vt.edu wrote: On 6/23/15 7:13 AM, Timofey Tyugashev wrote: I'm trying a few simulations of a

[gmx-users] GMX_LARGEFILES looks ignored in cmake of gromacs-5.0.5

Dear Mark and Roland: Thank you for response. Why did you decide to try to set it? Why do you ask? What do you try to achieve? For me, I found it is necessary to compile gromacs with MinGW32 on 32bit windows PC. Up to gromacs-4.6.7, it works without any troubles for me (see