[gmx-users] Which method for choosing concentration is more appropriate

Dear All, This is a general query regarding solvation of peptide in urea-water. My method is to place the peptide in the box first, add urea molecules using g_genbox and then solvate it using water molecules to maintain a desired concentration. There can be two approaches to this: 1) I can keep

[gmx-users] Regarding creating a itp for molecule from CGenFF

Hello all, I want to simulate methylamine with amino acid misture in CHARMM FF, so i have created methylamine in mol2 format and created the .itp and .pdb files from the CGenFF (which creates itp in CHARMM FF for GROMACS). and i have included it in topology file also as:- #Include

Re: [gmx-users] File forcefield.itp, line 4 Last line read: '[ defaults ]' Invalid order for directive defaults

I changed the order of .itp file and put the "topol_ATP.itp" ahead of protein.itp . However, I got the following errors this time: Fatal error: Syntax error - File forcefield.itp, line 6 Last line read: ' 11 no 1.0 1.0' Found a second defaults

[gmx-users] 5-letter atom names in topology files

Hi, Gromos 54a7 force field has built-in topologies for some small molecules, like ATP. In these topologies, many atoms have names of up to 5 letters, such as AO1PA and AO2PB. However, PDB files seem do not support 5-letter atom names. So, if I name an atom "AO2PB" in PDB, it will be

[gmx-users] File forcefield.itp, line 4 Last line read: '[ defaults ]' Invalid order for directive defaults

Dear All, I am setting up a simulation of protein-ATP complex. I manually combined the coordinates and topologies of the protein and ATP together, and ran editconf and solvate successfully. However, when I ran grompp, errors occurred: Syntax error - File forcefield.itp, line 4 Last line read:

[gmx-users] g_rdf and g_select for number of res with COM within distance to surface

Hi all, I'm trying to calculate the number of residues (part of a residue) within a distance (0.5 nm) to the surface of a molecule. The molecule (MOL) is made up of 43 atoms. The residues of interest are ASP (there's 36 of them in my system), but I'm only interested in the COM between OD1 and

Re: [gmx-users] Constraint vs. Umbrella in Pull COM

In the case of SHAKE constraint, there is no spring-like physics, like in umbrella pulling. The distance between COMs evolves according to the rate you set, but there is no COM oscillation around prescribed values, SHAKE turns the distance into a solid stick. Alex On Thu, Jun 22, 2017 at 5:13

[gmx-users] Constraint vs. Umbrella in Pull COM

Hi All, I was wondering if someone knows the difference between constraint versus umbrella pulling. I have read the manual but I'm still not sure what this means. 1. Umbrella pulling: A harmonic potential is applied between the centers of mass of two groups. Thus, the force is proportional

Re: [gmx-users] Computing work from pulling simulations

On Jun 21, 2017, at 2:32 AM, Leandro Bortot wrote: > > Have you compared the results of your calculation using the forces at > different intervals? e.g. every 1, 10, 50, 100 steps ? > > As long as you use a not-so-large interval the result should be the same > within

Re: [gmx-users] System shrinkage during vacuum simulation

On 22/06/17 20:03, Sanim Rahman wrote: Hello everyone, I ran a short MD simulation with a 3dc ewald geometry to simulate a vacuum slab at the top and bottom of my bilayer system. I equilibrated my system, tripled the size of my system in the z-direction and then added the 3dc geometry. My mdp

[gmx-users] System shrinkage during vacuum simulation

Hello everyone, I ran a short MD simulation with a 3dc ewald geometry to simulate a vacuum slab at the top and bottom of my bilayer system. I equilibrated my system, tripled the size of my system in the z-direction and then added the 3dc geometry. My mdp script is written as below: title =

Re: [gmx-users] Pulling inside a channel to calculate the PMF

I've never used PLUMED, to be honest, so I don't know. If ligands are salt ions or any other overall charged entities, I would solvate the channel (with restraint, maybe) for essentially a production run and apply an electric field "parallel" to the channel lumen, then just visualize the

Re: [gmx-users] How to get the correct reference frame to run the rmsf?

On 6/22/17 12:09 PM, ZHANG Cheng wrote: Dear Gromacs, I try to use this command to calculate RMSF: echo 3 | gmx rmsf -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsf_20-30ns.xvg -oq bfac.pdb -res -b 2 -e 3 My simulation lasts for 30 ns, but I only want RMSF for the last 10 ns. It is

[gmx-users] How to get the correct reference frame to run the rmsf?

Dear Gromacs, I try to use this command to calculate RMSF: echo 3 | gmx rmsf -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsf_20-30ns.xvg -oq bfac.pdb -res -b 2 -e 3 My simulation lasts for 30 ns, but I only want RMSF for the last 10 ns. It is mandatory to assign a reference frame, so I use

Re: [gmx-users] Regarding the charge of the atom in the .rtp file

On 6/22/17 11:23 AM, Dilip H N wrote: No, its not related to parameterization methodology. it is a different question... how can i identify the molecule as methylamine (for example) since in the .rtp the molecule type is written as [MAM1] [ MAM1 ] [ atoms ] N1 NG321-0.990 0

Re: [gmx-users] Regarding the charge of the atom in the .rtp file

No, its not related to parameterization methodology. it is a different question... how can i identify the molecule as methylamine (for example) since in the .rtp the molecule type is written as [MAM1] [ MAM1 ] [ atoms ] N1 NG321-0.990 0 C1 CG3AM2 -0.060 1 HN1 HGPAM2

Re: [gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates

Hi, On Thu, Jun 22, 2017 at 3:57 PM Diez Fernandez, Amanda < amanda.die...@imperial.ac.uk> wrote: > Hi Mark, > > Thanks. > > >mdrun will generally "make molecules whole" for -c, but otherwise doesn't > >care. Implementing general triclininc 3D periodicity with domain > >decomposition is a messy

Re: [gmx-users] Plotting Density Over Time?

On 6/22/17 9:53 AM, Sanim Rahman wrote: Hello everyone, I am curious if there is a feature in g_density that will allow me to calculate the density of my system at every single frame. I am hoping to track density change over time to calculate membrane thickness (peak to peak of electron

Re: [gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates

Hi Mark, Thanks. >mdrun will generally "make molecules whole" for -c, but otherwise doesn't >care. Implementing general triclininc 3D periodicity with domain >decomposition is a messy business. I am not using a triclinic unit cell (all angles are 90 in the input .pdb file). Wouldn¹t the

Re: [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

Thank Justin. Mark you are right. I did not think about to check the manual. Thanks again. > On 22 Jun 2017, at 15:51, Mark Abraham wrote: > > Hi, > > I'd start by looking in the documentation. Section 5.3.2 of the manual > clearly suggests putting it in the

[gmx-users] Plotting Density Over Time?

Hello everyone, I am curious if there is a feature in g_density that will allow me to calculate the density of my system at every single frame. I am hoping to track density change over time to calculate membrane thickness (peak to peak of electron density profile) and its standard deviation.

Re: [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

Hi, I'd start by looking in the documentation. Section 5.3.2 of the manual clearly suggests putting it in the ffnonbonded.itp file, which is where you expected to find it at the start of this thread, right? :-) Mark On Thu, Jun 22, 2017 at 3:47 PM gozde ergin wrote: >

Re: [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

On 6/22/17 9:47 AM, gozde ergin wrote: Hey Justin, I figured out how they calculated the sigma values. Basically they just take the geometric mean of nitrogen and oxygen sigma and epsilon from ffnonbed.itp file in OPLS-AA force field and calculated the pairwise LJ for N-O interaction. Now I

Re: [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

Hey Justin, I figured out how they calculated the sigma values. Basically they just take the geometric mean of nitrogen and oxygen sigma and epsilon from ffnonbed.itp file in OPLS-AA force field and calculated the pairwise LJ for N-O interaction. Now I also try to add this information in my

Re: [gmx-users] Domain decomposition

Thanks! I reduced the number to 4, and it works: gmx mdrun -v -dds 0.37 -nt 4 Cheers Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47

Re: [gmx-users] Domain decomposition

On 6/22/17 9:22 AM, Sergio Manzetti wrote: Checked the link, nothing written here on rcon and dds... "Thus it is not possible to run a small simulation with large numbers of processors." Google will help you find more suggestions. -Justin --

Re: [gmx-users] MDP for DNA with ions

On 6/22/17 9:21 AM, Sergio Manzetti wrote: Justin, I fixed the sim.mdp, however I realized I sent you the wrong mdp file, the one that gave DNA minimization problem is the EM.mdp Which is this: define = integrator = steep emtol = 100.0 emstep = 0.001 nsteps = 10 ; output frequency

Re: [gmx-users] Domain decomposition

Checked the link, nothing written here on rcon and dds... Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [

Re: [gmx-users] MDP for DNA with ions

Justin, I fixed the sim.mdp, however I realized I sent you the wrong mdp file, the one that gave DNA minimization problem is the EM.mdp Which is this: define = integrator = steep emtol = 100.0 emstep = 0.001 nsteps = 10 ; output frequency nstxout = 50 nstvout = 0 nstfout = 0

Re: [gmx-users] Domain decomposition

On 6/22/17 9:16 AM, Sergio Manzetti wrote: Hi, I have (also) a system of one molecule in water box of 3 3 3 dimensions, the procedure goes well all the way till the simulation starts, getting: Will use 20 particle-particle and 4 PME only ranks This is a guess, check the performance at the

[gmx-users] Domain decomposition

Hi, I have (also) a system of one molecule in water box of 3 3 3 dimensions, the procedure goes well all the way till the simulation starts, getting: Will use 20 particle-particle and 4 PME only ranks This is a guess, check the performance at the end of the log file

Re: [gmx-users] MDP for DNA with ions

OK, thanks for this! Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab  ] | [

Re: [gmx-users] MDP for DNA with ions

On 6/22/17 9:09 AM, Sergio Manzetti wrote: I use the AMBER99SB-ILDN ff for a piece of DNA taken from the RCSB database. Removed all waters and non-nucleic acid molecules, and everything seems fine. The mdp settings are: title = DNA in water stabilization cpp = /lib/cpp include = -I../top

Re: [gmx-users] MDP for DNA with ions

I use the AMBER99SB-ILDN ff for a piece of DNA taken from the RCSB database. Removed all waters and non-nucleic acid molecules, and everything seems fine. The mdp settings are: title = DNA in water stabilization cpp = /lib/cpp include = -I../top define = integrator = md dt = 0.002

Re: [gmx-users] MDP for DNA with ions

On 6/22/17 8:56 AM, Sergio Manzetti wrote: HI, I use mdp for simulating with a 2fs time step, nstlist 10, rlist 1.2, rcoulomb 1.2, rvdw 1.2, V-rescale, no P-coupling. Lincs on all bonds, still the DNA system won't minimize . What is your experience with DNA simulations and these settings?

Re: [gmx-users] Genion

Indeed. Thanks! Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/

Re: [gmx-users] Simulation of Carbon nanotube

On 6/22/17 8:31 AM, Nikhil Maroli wrote: Thanks, I have given the image of the system in the below link. I thought if I can get Topology and Parameters for CNT alone would be better to go with Charmm-gui. Since I can treat CNT as ligand and upload the parameters will work with the server so

Re: [gmx-users] Simulation of Carbon nanotube

Thanks, I have given the image of the system in the below link. I thought if I can get Topology and Parameters for CNT alone would be better to go with Charmm-gui. Since I can treat CNT as ligand and upload the parameters will work with the server so in this aspects any suggestion? like how to

Re: [gmx-users] Genion

THanks Justin. Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ |

Re: [gmx-users] Genion

Hi, The error message has a helpful URL that'll take you to the same advice that we give several times a week on here :-) Mark On Thu, 22 Jun 2017 14:27 Sergio Manzetti wrote: > Thanks, Worked out. Now I got a note saying: > > NOTE 1 [file em.mdp]: > The group

Re: [gmx-users] Genion

On 6/22/17 8:22 AM, Sergio Manzetti wrote: Thanks, Worked out. Now I got a note saying: NOTE 1 [file em.mdp]: The group cutoff scheme is deprecated since GROMACS 5.0 and will be removed in a future release when all interaction forms are supported for the verlet scheme. The verlet scheme

Re: [gmx-users] Genion

Thanks, Worked out. Now I got a note saying: NOTE 1 [file em.mdp]: The group cutoff scheme is deprecated since GROMACS 5.0 and will be removed in a future release when all interaction forms are supported for the verlet scheme. The verlet scheme already scales better, and it is compatible

Re: [gmx-users] Genion

On 6/22/17 8:14 AM, Sergio Manzetti wrote: OK, now I treied writing Na Cl and not NA and CL and get: This is what you did before, so naturally you get the same thing. Na) Warning: atom name 11966 in topol.top and dna_solv_NaCl.gro does not match (NA - Na) Warning: atom name 11967 in

Re: [gmx-users] Genion

OK, now I treied writing Na Cl and not NA and CL and get: Na) Warning: atom name 11966 in topol.top and dna_solv_NaCl.gro does not match (NA - Na) Warning: atom name 11967 in topol.top and dna_solv_NaCl.gro does not match (NA - Na) Warning: atom name 11968 in topol.top and dna_solv_NaCl.gro

Re: [gmx-users] Simulation of Carbon nanotube

On 6/22/17 6:59 AM, Nikhil Maroli wrote: Dear Justin, I have generated topology for CNT using gmx x2top. There is cyclic peptide nanotube wrapped over the CNT (eight CP rings in equal intervals) otherwise let's say, CNT is inserted into the Cyclic peptide nanotube. I wanted to put the whole

Re: [gmx-users] Genion

On 6/22/17 7:30 AM, Sergio Manzetti wrote: Hi, the procedure as defined by Juistin worked out well. However, a new problem has occurred. At mdrun for the minimization, I get: --- Program gmx mdrun, VERSION 5.1.2 Source code file:

Re: [gmx-users] Genion

Hi, the procedure as defined by Juistin worked out well. However, a new problem has occurred. At mdrun for the minimization, I get: --- Program gmx mdrun, VERSION 5.1.2 Source code file:

Re: [gmx-users] How to perform final MD simulation after extending a NPT simulation

Hi, On Wed, Jun 21, 2017 at 3:24 AM Adarsh V. K. wrote: > Dear all, > > *I used following command to extend a NPT simulation* > > 1) gmx convert-tpr -s npt.tpr -extend 500 -o tpxout.tpr > gmx mdrun -deffnm tpxout -cpi npt.cpt -v > > but the analysis "

Re: [gmx-users] (no subject)

Hi, I suggest you ask the authors of the tools, having checked their documentation. Mark On Wed, Jun 21, 2017 at 6:36 AM Shivangi Agarwal < shivangi.agarwal...@gmail.com> wrote: > Hello all > > How to handle HS14 generated by ATB server in topology file? > > > Regards > -- > Gromacs Users

Re: [gmx-users] positive potential energy

Hi, On Thu, Jun 22, 2017 at 11:30 AM Emran Heshmati wrote: > Hi all > I run two simulations on a 16 aa peptide under the same conditions > (forcefield, simulation duration, ...) except the solvent in one of > the simulations was TFE instead of water. The potential energy in

Re: [gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates

Hi, On Thu, Jun 22, 2017 at 11:05 AM Diez Fernandez, Amanda < amanda.die...@imperial.ac.uk> wrote: > Hi Mark, > Thank you for your reply. > > It is exactly the opposite though: OK, I understood the images the other way around, without titles. > for output_coordinates.gro which is the >

Re: [gmx-users] Regarding the charge of the atom in the .rtp file

Hi, I don't understand what you are asking. How does it relate to parameterization methodology? Mark On Thu, Jun 22, 2017 at 7:20 AM Dilip H N wrote: > Thank you for reply.. > > But how can i identify the molecule as methylamine (for example) since in > the .rtp the

Re: [gmx-users] Simulation of Carbon nanotube

Dear Justin, I have generated topology for CNT using gmx x2top. There is cyclic peptide nanotube wrapped over the CNT (eight CP rings in equal intervals) otherwise let's say, CNT is inserted into the Cyclic peptide nanotube. I wanted to put the whole system into the lipid bilayer. I was using

[gmx-users] positive potential energy

Hi all I run two simulations on a 16 aa peptide under the same conditions (forcefield, simulation duration, ...) except the solvent in one of the simulations was TFE instead of water. The potential energy in the TFE containing system was positive (about 14 Kj/mol), while in water containing

Re: [gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates

Hi Mark, Thank you for your reply. It is exactly the opposite though: for output_coordinates.gro which is the output from: mdrun Š -c output_coordinates.gro it seems like atoms are diffusing out of the box. In the trajectory, I allow atoms to be seen to diffuse out of the box, using -pbc

Re: [gmx-users] Pulling inside a channel to calculate the PMF

Hi Alex, There is no confusion about the pulling that is only a preparation for WHAM, but as you tell it you need to choose positions. These positions could be choosen manually: if one choose to explore the static channel from apo, then I'm agree, select the positions in the channel "in a bunch

Re: [gmx-users] Pulling inside a channel to calculate the PMF

I think your problem is solvable with enough perseverance, but there may also be some confusion... The PMF calculation isn't based on the data obtained from an actual pull: the pulling rate in those simulations is set to zero. The reason for using pull code there is to pull (pun intended) the

[gmx-users] Pulling inside a channel to calculate the PMF

Hi everybody, I would like to pull a ligand in a channel from my protein and calculate the PMF with Umbrella sampling. This channel is probably not linear and thus have to be defined. Too much colisions appears along a simple one axis pulling and causing a catastrophic PMF calculation. Currently