Re: [gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

this is the rest of the error message.. regards, Husen Halting parallel program gmx mdrun on rank 0 out of 16 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 Fatal error in PMPI_Bcast: Unknown error class, error stack: PMPI_Bcast(1635)..:

Re: [gmx-users] Problem in rmsf calculation

If you have selected C-alpha atoms on x-axis rmsf tool will write C-alpha atom index number so that is why you do not see 1-143. Run a gawk on your RMSF output to set the column 1 right. On 16 June 2016 at 10:48, Seera Suryanarayana wrote: > Dear gromacs users, > >

[gmx-users] Problem in rmsf calculation

Dear gromacs users, After mdrun I have plotted the rmsf for C-alpha atoms. My protein has 143 C-alpha atoms and I expected only that number in the plot. But I got rmsf values for all atoms of the protein(more than 2250 atoms). I have attached the plot for more information. What could be the

[gmx-users] Build time/Build user mismatch, fatal error truncation of file *.xtc failed

Hi all, I got the following error message when I tried to restart gromacs simulation from checkpoint file. I restart the simulation using fewer nodes and processes, and also I exclude one node using '--exclude=' option (in slurm) for experimental purpose. I'm sure fewer nodes and processes are

Re: [gmx-users] Simple gas-phase minimization help

On 6/15/16 4:46 PM, Tarick E wrote: Thanks for the help! I am following the Lysozyme tutorial except I am not solvating with water or balancing the charge with counter ions. When generating my .tpr with grompp, I am receiving the error: ERROR 1 [file minim_nick_edit1.mdp]: With Verlet

Re: [gmx-users] Simple gas-phase minimization help

Thanks for the help! I am following the Lysozyme tutorial except I am not solvating with water or balancing the charge with counter ions. When generating my .tpr with grompp, I am receiving the error: ERROR 1 [file minim_nick_edit1.mdp]: With Verlet lists only full pbc or pbc=xy with walls is

Re: [gmx-users] Lipid parameterization

On 6/15/16 12:27 PM, Christopher Neale wrote: Dear Justin, thank you for the clarification. I wonder, however, how "highly optimized" are all of the charmm36 lipid parameters for headgroups other than PC and PE? The JPCB 2010 paper doesn't mention PG, PS, or PA headgroups at all (as far as I

Re: [gmx-users] Calculating Dielectric constant

So instead of using epsilon-surface = 70, I should use its value equal to 1 ? By deault epsilon-surface = 0 which means it is turned off, to turn it on one must specify a value, as mentioned in Gromacs mdp options: "value of the relative permittivity of the imaginary surface around your infinite

Re: [gmx-users] PMF steadily increasing

(1) Are the protein and peptide really never interacting at d=7 nm? I presume you've got a peptide that would be maybe 5 nm long when fully extended, and your dG minimum is at 1.5 nm, so giving half the peptide length that would imply possible contact at 4 nm, so I expect 7 nm is sufficient,

[gmx-users] PMF steadily increasing

Dear GROMACS community, I performed umbrella sampling study to estimate the binding free energy between a globular protein with 568 residues and a small peptide with 13 residues. I use the pull code with k = 800 and rate = 0.005 to generate the initial conformations over the time course of 1200

Re: [gmx-users] Lipid parameterization

Dear Justin, thank you for the clarification. I wonder, however, how "highly optimized" are all of the charmm36 lipid parameters for headgroups other than PC and PE? The JPCB 2010 paper doesn't mention PG, PS, or PA headgroups at all (as far as I could tell), and Klauda's Mol Sim. 2015 paper

Re: [gmx-users] grompp not enough parameters

Thanks a lot ... I feel really dumb here ~~ Marlon Sidore PhD Student Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM) CNRS - UMR7255 31, Chemin Joseph Aiguier 13402 cedex 20 Marseille France 2016-06-15 17:26 GMT+02:00 Justin Lemkul : > > > On 6/15/16 11:07 AM,

Re: [gmx-users] Simulation in Constant pH simulation ...

Just to clarify. What Justin is suggesting is not a constant-pH MD simulation (as the protonation states won't be allowed to change during the simulation as explained), but it might be a good starting point to understand if different (fixed) protonation states will affect the properties of your

Re: [gmx-users] Simulation in Constant pH simulation ...

On 6/15/16 11:49 AM, Nikhil Maroli wrote: Hi, Justin , thanks for your reply. Actually, my system is cyclic peptide nanotube in water,which I made using charmm-gui. Protonation option availbe in " PDB reader " but how to confirm the pH,based on protonation ? or is it possbile to make any

Re: [gmx-users] Simulation in Constant pH simulation ...

Hi, Justin , thanks for your reply. Actually, my system is cyclic peptide nanotube in water,which I made using charmm-gui. Protonation option availbe in " PDB reader " but how to confirm the pH,based on protonation ? or is it possbile to make any changed after getting the out put -- Gromacs

Re: [gmx-users] electrophysiology builder

Hi, Thanks -- 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

Re: [gmx-users] Simulation in Constant pH simulation ...

On 6/15/16 11:34 AM, Nikhil Maroli wrote: Hi, I saw that already. in yasara software, they assign the protonation states of amino acids and ligands depending on the chosen pH.i know that that classical MD does not include dissociation and reassociation of protons, so residues will not change

Re: [gmx-users] Simulation in Constant pH simulation ...

Hi, I saw that already. in yasara software, they assign the protonation states of amino acids and ligands depending on the chosen pH.i know that that classical MD does not include dissociation and reassociation of protons, so residues will not change their protonation states during the MD.

Re: [gmx-users] electrophysiology builder

> On 15 Jun 2016, at 17:12, Nikhil Maroli wrote: > > Dear all, > I wanted to study the transport properties of channel protein in the lipid > bilayer.is there any server or tool to make sandwiches of the lipid bilayer > for studying the transport properties. The supporting

Re: [gmx-users] Fwd: Re: Dimeric structure strangely separated

On 6/15/16 10:25 AM, Pedro Lacerda wrote: Very thank you, Justin. So is just the system that is very unstable. Not necessarily. Have you tried fitting with trjconv? I haven't gotten a clear answer on that. Forget VMD centering, gmx rms -nopbc, etc. Have you used trjconv and gotten a

[gmx-users] grompp not enough parameters

Hi Marlon, If you change the comma into a point in the force constant values it should work Good luck Hello, I'm trying to use the amber03 ff to simulate a protein with iron clusters. I got the right parameters from a paper but then grompp tells me: "ERROR 1 [file

Re: [gmx-users] grompp not enough parameters

On 6/15/16 11:07 AM, Marlon Sidore wrote: Hello, I'm trying to use the amber03 ff to simulate a protein with iron clusters. I got the right parameters from a paper but then grompp tells me: "ERROR 1 [file clusters_ffbonded.itp, line 53]: Not enough parameters ERROR 2 [file

Re: [gmx-users] Gromacs 5.1 insert-molecules - Generating bad contacts?

Hi, Likely you're just generating clashes and sometimes getting lucky, e.g because your vdW radii is guessed badly if you don't manage it. Mark On Wed, 15 Jun 2016 17:10 Dan Gil wrote: > Hi, > > I am upgrading from gromacs 4.6 to gromacs 5.1. Gromacs 4.6 had "genbox," >

Re: [gmx-users] Simulation in Constant pH simulation ...

Nikhil, You might want t check this link to start with: http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation. Also a simple google search "GROMACS Constant pH MD" should give you some idea of the available options. Regards, On 15 June 2016 at 16:08, Nikhil Maroli

[gmx-users] electrophysiology builder

Dear all, I wanted to study the transport properties of channel protein in the lipid bilayer.is there any server or tool to make sandwiches of the lipid bilayer for studying the transport properties. -- Regards, Nikhil Maroli -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Simulation in Constant pH simulation ...

Dear all, I wanted to do MD in different pH such as 2,4,6,7.4,8,10,12 to check the stability of the peptide in the different pH environment. What is the possibility in Gromacs ? any keyword or method to set fixed pH? -- Regards, Nikhil Maroli -- Gromacs Users mailing list * Please search the

[gmx-users] Gromacs 5.1 insert-molecules - Generating bad contacts?

Hi, I am upgrading from gromacs 4.6 to gromacs 5.1. Gromacs 4.6 had "genbox," which I was able to use without a problem. With gromacs 5.1, I am using insert-molecules to generate my initial configuration containing water, ethanol, and a lennard-jones particle which I defined. When I attempt to

[gmx-users] grompp not enough parameters

Hello, I'm trying to use the amber03 ff to simulate a protein with iron clusters. I got the right parameters from a paper but then grompp tells me: "ERROR 1 [file clusters_ffbonded.itp, line 53]: Not enough parameters ERROR 2 [file clusters_ffbonded.itp, line 54]: Not enough parameters

Re: [gmx-users] Regarding installation in gpu

Hi, There's no GNU compiler that can install 4.6.2 that cannot install 5.1 ;-) And if there was, you surely want all the bug fixes leading to 4.6.7... Mark On Wed, Jun 15, 2016 at 4:10 PM SOUVIK MONDAL wrote: > The gnu compiler version is low that is why I am trying to

Re: [gmx-users] Fwd: Re: Dimeric structure strangely separated

Very thank you, Justin. So is just the system that is very unstable. Noob questions follows. But here other similar system where shows what I expect when the molecule is across the boundary. This isn't happening in the previous plot. gmx rms -s md.tpr -f md.xtc -pbc

Re: [gmx-users] Average exchange probability when extending REMD

Hi, Yes, if you need that, this is the thing to do. The only place mdrun records any of that is the .log file, and of course that is not re-read in the next stage.You also want to avoid/manage mdrun's appending feature, because IIRC that throws away all that end-of-log-file output when the next

Re: [gmx-users] Regarding installation in gpu

On 6/15/16 9:58 AM, SOUVIK MONDAL wrote: The gnu compiler version is low that is why I am trying to install version 4.6.2. "Maybe need administrative privileges." Does it mean that I need root permission? Re-read my previous message :) -Justin - Original Message - From: "Justin

Re: [gmx-users] Regarding installation in gpu

The gnu compiler version is low that is why I am trying to install version 4.6.2. "Maybe need administrative privileges." Does it mean that I need root permission? - Original Message - From: "Justin Lemkul" To: gmx-us...@gromacs.org Sent: Wednesday, June 15, 2016 4:57:07

Re: [gmx-users] Fwd: Re: Dimeric structure strangely separated

On 6/15/16 9:49 AM, Pedro Lacerda wrote: PBC is always considered by default at Gromacs analysis tools, and I recentered following the standard VMD procedure. Considering the PBC, the animation looks quite right to me. Well, sure - PBC doesn't care about visualization convenience, but the

Re: [gmx-users] Fwd: Re: Dimeric structure strangely separated

PBC is always considered by default at Gromacs analysis tools, and I recentered following the standard VMD procedure. Considering the PBC, the animation looks quite right to me. Can a .top file have a molecule where not all atoms are bonded? 2016-06-15 10:39 GMT-03:00 Justin Lemkul

Re: [gmx-users] Average exchange probability when extending REMD

Sorry, I am a little confused, what you mean is that the gromacs cannot automatically combine the data of the both in the replica exchange statistics section. Maybe myself need write some program to combine the first part data and the extended data to get the average probability of whole

Re: [gmx-users] Fwd: Re: Dimeric structure strangely separated

On 6/15/16 9:35 AM, Pedro Lacerda wrote: Thank you, I never did it before but I'll try it. And at VMD I recentered the molecule. And looks right to you so much deviation even at the begining? Never happened to me! You're calculating the RMSD of a broken molecule; the animation shows that

Re: [gmx-users] Fwd: Re: Dimeric structure strangely separated

Thank you, I never did it before but I'll try it. And at VMD I recentered the molecule. And looks right to you so much deviation even at the begining? Never happened to me! One more question. What happens when two molecules are put as one molecule in .top, like a molecule that are two disjoints

Re: [gmx-users] Average exchange probability when extending REMD

Hi, That's never been implemented, unfortunately. Mark On Wed, Jun 15, 2016 at 3:25 PM OuyangYanhua <15901283...@163.com> wrote: > Hi, > I extended the REMD of a protein in a explicit water and append the data > to the old ones and it appended. However, at the end of the .log files, the >

[gmx-users] Average exchange probability when extending REMD

Hi, I extended the REMD of a protein in a explicit water and append the data to the old ones and it appended. However, at the end of the .log files, the replica exchange statistics section only contains the data of extended time, it did not combine the former statistics and the extended

Re: [gmx-users] net charge correction

Hi, On Wed, Jun 15, 2016 at 12:05 PM Michael Brunsteiner < michael.brunstei...@tugraz.at> wrote: > > Hi, > > In an attempt to understand how gromacs deals with electrostatic > (long range) interactions in systems with a net-charge i made couple > of simple model systems > Calculating the

Re: [gmx-users] Fwd: Re: Dimeric structure strangely separated

On 6/15/16 8:45 AM, Pedro Lacerda wrote: Hi list, RMSD analysis of trajectories differs very much from the intuition gained with the visual inspection of trajectories. RMSD has almost 4nm while the video seems correct. I'm using Amber 14ffSB with an metallic nonbonded ion attached on it. It

[gmx-users] Fwd: Re: Dimeric structure strangely separated

Hi list, RMSD analysis of trajectories differs very much from the intuition gained with the visual inspection of trajectories. RMSD has almost 4nm while the video seems correct. I'm using Amber 14ffSB with an metallic nonbonded ion attached on it. It was converted from Amber files using ACPYPE,

Re: [gmx-users] Something weird with shell particle dynamics

Just solved the problem! I have seen one of your comments justin and i fixed it! Thank yoi really much! Il 15/Giu/2016 13:28, "Justin Lemkul" ha scritto: > > > On 6/15/16 5:06 AM, Luca Banetta wrote: > >> Dear all gromacs users, >> >> I am trying to run a shell molecular

Re: [gmx-users] Calculating Eccentricity

Dear Sanket, Removing periodicity is difficult if SDS molecules transiently leave the micelle and return after having moved one or more unit cells. You might want to try using gmx clustsize to generate snapshots along the trajectory and use trjconv on them to put all molecules in the same unit

Re: [gmx-users] h_bond

On 6/15/16 3:23 AM, Shahid Nayeem wrote: Dear all I want to get number of hydrogen bonds between solvent(water) and alpha helix or beta sheet along the trajectory. Secondary structure of protein changes along the trajectory. Is it possible for gromacs to first find the secondary structure of

Re: [gmx-users] Something weird with shell particle dynamics

On 6/15/16 5:06 AM, Luca Banetta wrote: Dear all gromacs users, I am trying to run a shell molecular dynamics simulation using GROMACS version 4.6.5. First of all a shell particle has been introduced in an OPLS-AA force field. Unfortunately, immediately after the mdrun has been started

Re: [gmx-users] Regarding installation in gpu

On 6/15/16 7:06 AM, SOUVIK MONDAL wrote: Hi I got the following error during gromacs4.6.2 installation(parallel ver) in gpu. Error : Install the project... -- Install configuration: "Release" CMake Error at cmake_install.cmake:44 (file): file cannot create directory:

Re: [gmx-users] Open-closed transition in a dimeric enzyme, WTM simulations

Dear Tarak, My guess is that your reaction coordinate is ill-chosen and that it fails to capture some significant transitions in orthogonal directions. This can be difficult to know beforehand unfortunately. Kind regards, Erik > On 10 Jun 2016, at 19:09, tarak karmakar

[gmx-users] Regarding installation in gpu

Hi I got the following error during gromacs4.6.2 installation(parallel ver) in gpu. Error : Install the project... -- Install configuration: "Release" CMake Error at cmake_install.cmake:44 (file): file cannot create directory: /usr/local/gromacs/share/gromacs. Maybe need administrative

Re: [gmx-users] to neutralize the system

Thanks. If I got your point correctly, then how should I know the end states of the surface-binding process in advance before doing any simulation? And if I start the pre-simulation(just to find the end states) with one of the methods of neutralization, then this affects surely on end states!

Re: [gmx-users] to neutralize the system

Hi, So you need to choose a topology for the amino acid that is consistent with the end states of the surface-binding process (whatever that is). This drives the answer to the question of what methods for neutralization are feasible. Mark On Wed, Jun 15, 2016 at 12:06 PM Alexander Alexander <

Re: [gmx-users] to neutralize the system

Hello, The final goal is to model the adsorption behavior of a heptapeptide to a metal surface, and meanwhile, calculation of the single amino acid(involved in the peptide) binding free energy into the same surface. Some of the residues of amino acid are charged, however, their charge would get

[gmx-users] net charge correction

Hi, In an attempt to understand how gromacs deals with electrostatic (long range) interactions in systems with a net-charge i made couple of simple model systems Calculating the energy of a system with a SINGLE charge on only ONE atom in a periodic system with PME I get: gmx energy -f

Re: [gmx-users] How to add solvent in a Biphasic Systems ?

Hi, On Wed, Jun 15, 2016 at 5:49 AM Jinfeng Huang wrote: > Dear gromacs users, > > > I want to build a liquid-solid system following the tutorial "Building > Biphasic Systems" ( >

Re: [gmx-users] to neutralize the system

Hi, Such an answer starts with "what are you trying to model?" Mark On Wed, Jun 15, 2016 at 11:45 AM Alexander Alexander < alexanderwie...@gmail.com> wrote: > Hello, > > How about neutralization of these cases, a single amino acid (zwitterionic > form) > or a peptide in aqueous solution; > I

Re: [gmx-users] to neutralize the system

Hello, How about neutralization of these cases, a single amino acid (zwitterionic form) or a peptide in aqueous solution; I was wondering which of below methods is preferable for neutralizing the system? One is the introducing a counter-ion(Na or Cl for example) and the second one is the

Re: [gmx-users] Something weird with shell particle dynamics

Hi, I have no idea about this code, but you might have more luck when starting new work choosing a recent version, which may have bugs fixed... Mark On Wed, Jun 15, 2016 at 11:06 AM Luca Banetta wrote: > Dear all gromacs users, > > I am trying to run a shell molecular

[gmx-users] Something weird with shell particle dynamics

Dear all gromacs users, I am trying to run a shell molecular dynamics simulation using GROMACS version 4.6.5. First of all a shell particle has been introduced in an OPLS-AA force field. Unfortunately, immediately after the mdrun has been started this fatal error appeared: “Something weird

Re: [gmx-users] Calculating Eccentricity

Hi Sanket, You probably want the clustering routine of trjconv. And then calculate the principal axes of the micelle. The instantaneous value does not mean much, but a an average non-zero eccentricity would suggest with a greater extent than without peptide would suggest an effect. Note that you

[gmx-users] h_bond

Dear all I want to get number of hydrogen bonds between solvent(water) and alpha helix or beta sheet along the trajectory. Secondary structure of protein changes along the trajectory. Is it possible for gromacs to first find the secondary structure of snapshot and then calculate hydrogen bonds

[gmx-users] Calculating Eccentricity

Dear gmx user I am performing a MD simulation of peptides in sds for 100ns. After the completion of my production I am unable to remove the periodic boundary condition. I wanted to Calculate the eccentricity of the SDS micelle after 100ns, does the periodic boundary condition affect my