Re: [gmx-users] PBC after energy minimization

On 5/1/20 9:29 AM, John Whittaker wrote: Hi Mohamed, Hello everybody, In order to solve the PBC at the end I use the command: *gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_noPBC.xtc -pbc mol * followed by: *gmx trjconv -s md_0_1.tpr -f md_noPBC.xtc -o md_noPBC.pdb* I want to solve

Re: [gmx-users] PBC after energy minimization

Hi Mohamed, > Hello everybody, > > In order to solve the PBC at the end I use the command: > > *gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_noPBC.xtc -pbc mol * > > followed by: > > *gmx trjconv -s md_0_1.tpr -f md_noPBC.xtc -o md_noPBC.pdb* > > > I want to solve this problem after the energy

Re: [gmx-users] pbc nojump with replica exchange behaves differently than with regular MD

On 11/28/19 11:04 AM, Ramon Crehuet wrote: Dear Justin, Thanks for your suggestion. It works, as long as I set a tpr file in the -s option. So this works: gmx trjconv -f md.trr -s md.tpr -pbc mol -center -o whole.xtc But the following does not work (where whole_center.gro is a system

Re: [gmx-users] pbc nojump with replica exchange behaves differently than with regular MD

Dear Justin, Thanks for your suggestion. It works, as long as I set a tpr file in the -s option. So this works: gmx trjconv -f md.trr -s md.tpr -pbc mol -center -o whole.xtc But the following does not work (where whole_center.gro is a system without water molecules with a whole centered

Re: [gmx-users] pbc nojump with replica exchange behaves differently than with regular MD

On 11/28/19 9:44 AM, Ramon Crehuet wrote: Dear all, As a follow-up to my question, I have seen that in a regular MD, the coordinates of the original trajectory are always smaller than the unitcell vectors, whereas this is not true in the trajectory from the replica exchange (deviations up

Re: [gmx-users] pbc nojump with replica exchange behaves differently than with regular MD

Dear all, As a follow-up to my question, I have seen that in a regular MD, the coordinates of the original trajectory are always smaller than the unitcell vectors, whereas this is not true in the trajectory from the replica exchange (deviations up to 1.5%). Could this be confusing trajconv?

Re: [gmx-users] PBC conditions for Vacuum simulation

Hi, No. Models without cutoffs will scale badly with particle count. Adding cutoffs is not always a performance win either, because while that saves computation of interactions, it adds the need to periodically search for which particle interactions to compute. Mark On Sat., 9 Feb. 2019, 17:24

Re: [gmx-users] PBC fix for visualization

Hi Dallas and other Gromacs users, I used -pbc whole and -ur compact in the first step "System" index group And then, used the output file for -pbc cluster. Choosing the "System" index for clustering gave the best result I got. (Although there are still few lipids which are not completely in the

Re: [gmx-users] PBC

On 2/12/18 8:44 AM, Ahmed Mashaly wrote: Hi If I want to use gmx trjconv to recenter the protein in xtc file, the reference (-s) .tpr should be the one I used in simulation (md.tpr) or I can use the first one (em.tpr) without a difference? This is because the protein has jumped after em

Re: [gmx-users] Pbc

On 8/16/17 4:24 PM, farial tavakoli wrote: blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } Dear gromacs users I need to visualize my md_0_1.tpr , so i issued trjconv -s

Re: [gmx-users] PBC ISSUES IN GROMACS

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions had useful information Mark On Mon, 14 Aug 2017 09:17 Neha Gupta wrote: > Hi gromacs users, > > After simulation for 5 ns, I generated a movie.pdb file using .gro and .xtc > > However, in the

Re: [gmx-users] PBC ISSUES IN GROMACS

On 14/08/17 09:17, Neha Gupta wrote: Hi gromacs users, After simulation for 5 ns, I generated a movie.pdb file using .gro and .xtc However, in the movie file, I witnessed bizarre long bonds... How to fix it? Any suggestions please? trjconv -pbc whole Thanks, Neha -- David van der

Re: [gmx-users] PBC fix for visualization

Hi Dallas, Thanks for your reply. I did try -pbc cluster for waters. It could fix it somehow but not completely. After that, I had to use -pbc center to fix it. Still, I do not get what I want. Unfortunately, some waters and lipids are appearing from the other side of the box. Cheers, Mohsen

Re: [gmx-users] PBC fix for visualization

I have found the cluster option of -pbc to work well for putting aggregates back together correctly. Some times you do need an index file and appropriate groups to assist with it getting it right. gmx trjconv -pbc cluster Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash

Re: [gmx-users] PBC

On 5/5/17 1:37 PM, Alex wrote: Dear Gromacs user, I want to study the interaction between a nanoparticle(5 nm diameter) and some heptapeptide around the nanoparticle in aqueous solution. I put the nanoparticle in the center of a box and the rest are around it. I was wondering if I should use

Re: [gmx-users] PBC issues with membrane-peptide simulation

Dear users, Well, I have found another solution for avoiding the diffusion through the periodic boundary in such simulations. Hope this is helpful to others doing similar work. Basically, the idea is to apply a biasing potential to the COM of the peptides to pull them towards the membrane so as

Re: [gmx-users] PBC issues with membrane-peptide simulation

Sorry for that Mark. Basically, our experimental studies show that our designed peptides (2-3 different peptides) are involved in membrane destabilization but their activity (in terms of MIC values) varies. We want to understand the molecular underpinnings of the membrane destabilization process

Re: [gmx-users] PBC issues with membrane-peptide simulation

Hi, You haven't said what you're trying to model, so it's going to be hard for someone to help out :-) Mark On Thu, 10 Nov 2016 05:21 Abhi Acharya wrote: > Thank you Stephane for your suggestion. Though this seems like a nice > solution to circumvent the problem, but

Re: [gmx-users] PBC issues with membrane-peptide simulation

Thank you Stephane for your suggestion. Though this seems like a nice solution to circumvent the problem, but do you think this is the normal way to go about it? I have never found anyone reporting such a methodology for membrane peptide simulation. Also, I can anticipate significant increase in

Re: [gmx-users] -pbc nojump failure

Dear Irem, You may want to run the trajectory through trjconv and translate it, or use e.g. -pbc whole, so that the protein is intact at frame 1. Then you can run trjconv -pbc nojump on the resulting trajectory. This usually requires a bit of trial and error. Kind regards, Erik > On 31 Mar

Re: [gmx-users] -pbc nojump failure

I think the problem is that I can’t seem to start from an unfragmented structure. I start from the .pdb file, where the protein is a whole, and end up with a .tpr file that is fragmented. The interesting thing is, this did not happen with version 4.6.5 (I now use 5.1.2). Do I have to do

Re: [gmx-users] -pbc nojump failure

No! You can't do that, because fitting will cause the PBC and the coordinates to mismatch. So 'nojump' after that will for sure screw up the coordinates. Check the trjconv workflow on the Gromacs site. Cheers, Tsjerk On Mar 31, 2016 14:23, "Francesco Carbone" wrote: >

Re: [gmx-users] -pbc nojump failure

Hi, Thanks. If I do that, the reference structure would be what’s in the .tpr file, right? Best, Irem > On Mar 31, 2016, at 8:22 AM, Francesco Carbone wrote: > > You could try to fit first (-fit rot+trans) and fix pbc (-pbc nojump) later. > > Cheers, > > Fra > > On

Re: [gmx-users] -pbc nojump failure

Hi, Thanks for your suggestion. Unsurprisingly, the structure in nvt_water_frozen.tpr is also fragmented. Is there a way to use the input .pdb file as reference, somehow? Best, Irem > On Mar 31, 2016, at 12:45 AM, Tsjerk Wassenaar wrote: > > Hi Irem, > > Check the

Re: [gmx-users] -pbc nojump failure

You could try to fit first (-fit rot+trans) and fix pbc (-pbc nojump) later. Cheers, Fra On 31 March 2016 at 05:45, Tsjerk Wassenaar wrote: > Hi Irem, > > Check the structure in nvt_water_frozen.tpr: > > gmx editconf -f nvt_water_frozen.tpr -o ref.pdb > > Cheers, > > Tsjerk

Re: [gmx-users] -pbc nojump failure

Hi Irem, Check the structure in nvt_water_frozen.tpr: gmx editconf -f nvt_water_frozen.tpr -o ref.pdb Cheers, Tsjerk On Mar 31, 2016 00:04, "Irem Altan" wrote: > Hi, > > I am simulating a protein in its unit cell. I use the original .pdb file > as an input, so the

Re: [gmx-users] pbc

On 1/5/16 11:58 AM, Parvez Mh wrote: Dear all: I am using pbc in all directions, it is expected that, i will observe broken molecules in central box. But i am wondering, some molecules are out of box when i visualize with vmd. What would the right explanation of this? PBC is the

Re: [gmx-users] pbc

On 10/19/15 9:59 PM, Sana Saeed wrote: good morning gmx usersi want to visualize the box from my gro file. I am using VMD , i read the manual but couldnt understand how to use my own vectors to visualize box. actually i want to see if the atoms are out of box or inside.Thanks in advance

Re: [gmx-users] PBC

I thought so :D Thanks! On Thu, Oct 8, 2015 at 9:37 AM, mah maz wrote: > Hi Mark > > Thank you. I suppose grid can be used without PBC specially when the > system is in vacuum. > There are some parameters in the .mdp file that I haven't defined and I > don't want them to be

Re: [gmx-users] PBC

Hi, On Thu, Oct 8, 2015 at 8:08 AM mah maz wrote: > Hi Mark > > Thank you. I suppose grid can be used without PBC specially when the system > is in vacuum. > There are some parameters in the .mdp file that I haven't defined and I > don't want them to be applied during

Re: [gmx-users] PBC

Hi Mark Thank you. I suppose grid can be used without PBC specially when the system is in vacuum. There are some parameters in the .mdp file that I haven't defined and I don't want them to be applied during simulation. However in the mdout.mdp They are present eg. gen-seed, emtol, ewald-rtol,

Re: [gmx-users] PBC

Hi, I don't really remember. I suspect not, so I would look up the docs for ns-type, which should mention limitations, and otherwise try it out. grompp and/or mdrun are pretty good at complaining about things they can't do. Mark On Mon, Oct 5, 2015 at 12:56 PM mah maz

Re: [gmx-users] PBC

Hi Mark, Thanks. It seems the default is pbc =xyz. But my question is if I don't use PBC, can I use grid, or grid is only meaningful when PBC is defined? On Mon, Oct 5, 2015 at 11:07 AM, mah maz wrote: > Dear users, > > If I dont define pbc=no, what is the default type for

Re: [gmx-users] PBC

Hi, See top of http://manual.gromacs.org/documentation/5.1/user-guide/mdp-options.html regarding defaults. Or you can leave it blank and inspect what gmx grompp writes to the mdout.mdp. Whether any PBC setting makes sense depends what you're trying to do, which we don't know. Mark On Mon, Oct

Re: [gmx-users] PBC in a closed box.

choosing the electrostatic treatment seems to be the least of your problems: once you turn off the PBC, water molecules will coalesce into a spherical droplet in order to minimize the surface energy, so you first have to ask yourself if a nanometric water droplet suits your needs. Not a simulation

Re: [gmx-users] PBC issue

If you just want to make a new, larger water box, try editconf to make the box larger and then genbox to add water. Any help beyond than that requires us to guess at at least four questions: What is an unloading simulation How did you pull a protein What exactly do you mean by both ends of the

Re: [gmx-users] PBC problem in bilayer system

On 9/15/14 4:52 AM, shahab shariati wrote: Dear Tsjerk Thanks for your reply. I think that there is another problem, except for visualization. I obtained the Z coordinate (along the bilayer normal) of the center of mass of the 4 drug molecules (violet, blue, red and green lines) and DPPC

Re: [gmx-users] PBC problem in bilayer system

On 9/15/14 12:11 PM, shahab shariati wrote: Dear Justin Very very thanks for your time and consideration. Excuse me for many questions. I want to make sure my trajectory is valid and accurate for analysis and then for writing related paper. It is. My last question is that can I use

Re: [gmx-users] PBC problem in bilayer system

On 9/15/14 3:12 PM, shahab shariati wrote: Dear Justin Thanks for your answer. You said The raw output of g_traj in this case is not very useful I want to know position and location of drug molecules relative to the DPPC bilayer during simulation time. In your opinion, how should I use

Re: [gmx-users] PBC problem in bilayer system

On 9/13/14 7:59 AM, shahab shariati wrote: Dear Justin you said The -trans option takes a vector where you specify the amount of translation to apply I do not know what vector should be considered in -trans option. Well, what have you tried? You need to shift your system along z, the

Re: [gmx-users] PBC problem in bilayer system

On 9/14/14 8:43 AM, shahab shariati wrote: Dear Justin Thanks for your reply. I inserted 4 drug molecules in close vicinity to the membrane surface in water phase, in one side of bilayer (for example, top). In the different frames of trajectory, some of drug molecules (one or two drug

Re: [gmx-users] PBC problem in bilayer system

On 9/14/14 8:58 AM, shahab shariati wrote: Dear Justin I did MD simulation on the NPT ensemble: pcoupl = Berendsen pcoupltype = semiisotropic ref_p = 1.0 In this condition, to solve this problem, what should I do? I have already

Re: [gmx-users] PBC problem in bilayer system

On 9/14/14 9:52 AM, shahab shariati wrote: Dear Justin I did following: trjconv -f *.xtc -s *.tpr -n *.ndx -o **.xtc -trans 6.46063 6.57889 9 Based on your reply*, *I translated all system along the z. I used x and y according to box dimension. I used 9, instead of z dimension

Re: [gmx-users] PBC problem in bilayer system

On 9/14/14 10:29 AM, shahab shariati wrote: Dear Justin Based on your previous reply, I used following: trjconv -f *.xtc -s *.tpr -n *.ndx -o **.xtc -pbc mol –trans 0 0 7 When I see **.xtc using vmd, unfortunately, problem was not solved. Please see the following link:

Re: [gmx-users] PBC problem in bilayer system

Hi, Just a small side note. There's nothing intrinsically nonsensical about translating more than a box size. The PBC are translation invariant, so you can do anything and have the system be fine. However, for visualization, translating one box length, and put the stuff back in the box, makes as

Re: [gmx-users] PBC problem in bilayer system

On 9/11/14 8:01 AM, shahab shariati wrote: Dear gromacs users When I see trajectory file using vmd, there is state showed in following link: https://www.dropbox.com/s/g8i934atodrb7te/figure2.TIF?dl=0 in initial structure, all 4 drugs were inserted in water phase, in one side of bilayer.

Re: [gmx-users] PBC problem in bilayer system

Hi, Try -pbc nojump Best, Mike On 09/09/2014 15:11, shahab shariati shahab.shari...@gmail.com wrote: Dear gromacs users I did MD simulation of my system containing DPPC lipids + water molecule and 4 drug molecules. I saw trajectory file using VMD. Unfortunately, drug molecules jump across

Re: [gmx-users] PBC problem in bilayer system

Also if you want to fix the position on the centre of mass (no rotating or translating) try -pbc nojump Followed by -fit rot+trans Remember to use you new .xtc from your no jump command for the -fit command. Then view in vmd and your molecules will not jump, rotate, or translate around the box.

Re: [gmx-users] PBC problems??

On 5/23/14, 2:51 PM, Steve Seibold wrote: My protein breaks according to viewing the traj in VMD and graphing the RMSD of the protein C-terminus I have tried all combinations of trjconv -pbc -center -box center and nothing works..I was able to get online and find a tutorial that says

Re: [gmx-users] PBC correction to visualize a protein-membrane structure

Dear Justin, you’re right. The problem was the system was not center properly in the initial .gro file. Now it works. Thank you very much. Juan C. On 5/17/14, 5:49 AM, Juan Munoz-Garcia wrote: Dear Mark, I’ve used numbers. Just indicated them as x_box/2, etc to be clearer. There are two

Re: [gmx-users] PBC correction to visualize a protein-membrane structure

On 5/16/14, 4:04 AM, Juan Munoz-Garcia wrote: Dear GROMACS users, I’m preparing a protein-membrane structure to use as input for MD. I’ve just carried out a short minimisation of the lipids applying restraints to the protein, after which I’ve obtained the attached structure. I’ve tried all

Re: [gmx-users] PBC correction to visualize a protein-membrane structure

Thank you Justin, please find a dropbox link to the image below. I’ve used trjconv_mpi -f NPT.trr -o NPT_2.trr -s NPT.tpr -pbc whole trjconv_mpi -f NPT_2.trr -o NPT_PBC.trr -s NPT.tpr -pbc mol -ur compact -center and different combinations of those

Re: [gmx-users] PBC correction to visualize a protein-membrane structure

On 5/16/14, 9:08 AM, Juan Munoz-Garcia wrote: Thank you Justin, please find a dropbox link to the image below. I’ve used trjconv_mpi -f NPT.trr -o NPT_2.trr -s NPT.tpr -pbc whole trjconv_mpi -f NPT_2.trr -o NPT_PBC.trr -s NPT.tpr -pbc mol -ur compact -center and different combinations of

Re: [gmx-users] PBC correction to visualize a protein-membrane structure

Dear Justin, thank you. I’ve tried the following but neither of them worked, I get the same result. trjconv -f input.gro -o output.gro -s .tpr -trans 0 0 z_box/2 -pbc mol -ur compact trjconv -f input.gro -o output.gro -s tpr -trans x_box/2 y_box/2 z_box/2 -pbc mol -ur compact This is

Re: [gmx-users] PBC correction to visualize a protein-membrane structure

On May 16, 2014 7:03 PM, Juan Munoz-Garcia juan.munoz-gar...@bioch.ox.ac.uk wrote: Dear Justin, thank you. I’ve tried the following but neither of them worked, I get the same result. trjconv -f input.gro -o output.gro -s .tpr -trans 0 0 z_box/2 -pbc mol -ur compact trjconv -f input.gro

Re: [gmx-users] pbc problems

Hello everyone! I am a new one of gromacs. When a simulation of protein in water is finished, should i first use the command of trjconv to remove pbc conditions(with nojump or mol), and then began analyze the new trajectory(rmsd, Rg and some other parameters)? Is the result

Re: [gmx-users] PBC problem after MD

If there's a problem, trjconv can handle it with the use of the right index groups, as suggested at http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions. But it can't keep these three things together if there's no index group that describes these three things. You may need

Re: [gmx-users] PBC problem after MD

Dear Kannan, Thank you for your fast response. The problem is that the ligand is as far as 16 Ang., which is too far away from the coenzyme for any kind of bonding. here is the link for downloading my dist.jpeg file.http://we.tl/ACencjievC Do you think that this is a real PBC problem? Really

Re: [gmx-users] pbc problem

On 2/2/14, 7:15 AM, Atila Petrosian wrote: Dear Justin and Tsjerk you said Some tools handle PBC properly, some don't . I want to know exactly which tools of gromacs handle PBC properly. Can I find these tools in manual? No, because it's not possible to test every single command that

Re: [gmx-users] pbc

Thank you for your reply Tsjerk.. I do many Trjconv -pbc mol -ur compact -center. but it doesn't help.. this is PBC. if i center protein the ligand goes other side at end of simulation. if i center ligand, then protein goes... if i center both, its trajectory is same as old one. How to overcome

Re: [gmx-users] pbc

On 1/31/14, 7:09 AM, kannan wrote: Thank you for your reply Tsjerk.. I do many Trjconv -pbc mol -ur compact -center. but it doesn't help.. this is PBC. if i center protein the ligand goes other side at end of simulation. if i center ligand, then protein goes... if i center both, its

Re: [gmx-users] pbc

Thank you very much for your valuable suggestion Justin... best regards, kannan s I On Fri, Jan 31, 2014 at 6:31 PM, Justin Lemkul [via GROMACS] ml-node+s5086n5014192...@n6.nabble.com wrote: On 1/31/14, 7:09 AM, kannan wrote: Thank you for your reply Tsjerk.. I do many Trjconv -pbc

Re: [gmx-users] pbc problem

Hi, trjconv -s topol.tpr -f traj -pbc mol -o traj_modified select '0' for the entire system You can try using either 'mol' or 'nojump' depending on your visualization needs. cheers, Tarak On Wed, Jan 29, 2014 at 3:39 PM, Atila Petrosian atila.petros...@gmail.comwrote: Dear Gromacs users I

Re: [gmx-users] pbc problem

On 1/29/14, 9:13 AM, Atila Petrosian wrote: Dear Justin Thanks for your reply. To obtain modified trajectory and then comparing with original trajectory, I do not know exactly which of none, mol, res, atom, nojump, cluster or whole is appropriate for me. In a simple case like this, many