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 th

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 m

[gmx-users] PBC after energy minimization

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 minimization but I don't have .x

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 withou

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 prot

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 t

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? Co

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

Dear all, I have run a temperature replica exchange and I would like to analyze the resulting trajectory for a given temperature (i.e. not following a replica across temperatures using demux.pl). The simulations consist of a single protein chain. I can easily generate have a whole molecule, na

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 N

[gmx-users] PBC conditions for Vacuum simulation

Hello gromacs users, I am trying to model a peptide in gas phase which requires proper conditions like: no PBC, no cut-offs for VanderWaals and electrostatics, coulomb type not PME. However, this increases computational time by N^2 for N number of atoms. Is there a way to mitigate this? Many t

[gmx-users] PBC for ewald-geometry 3dc warning

Hi everyone, I am trying to simulate a crystal slab using 3dc Ewald correction and PBC in xyz with dimensions 3.5nm*4.4nm*3.2nm and with the box length of more than 3xZ in the z-direction with my slab in the center of the box, as recommended in GROMACS manual. I am getting the following warning:

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

[gmx-users] PBC problems related to comm-grps in membrane simulation?

Hi, I'm having difficulty with a membrane receptor simulation. It seems like whenever the receptor crosses the boundary (I'm using PBC), the box gets distorted so that the z axis is compressed from 10.2nm to 8-8.2nm which is too large a change. I was initially using System for the comm-grps optio

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 step

[gmx-users] PBC

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 step, and if I have to use md.tpr as reference f

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 md

[gmx-users] Pbc

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 md_0_1.tpr -f md_0_1.xtc -o xxx.pdb -pbc nojump -

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 movie file, I witnessed b

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 Spoe

[gmx-users] PBC ISSUES IN GROMACS

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? Thanks, Neha -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.or

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 On

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

[gmx-users] PBC fix for visualization

Dear Gromacs users, I have an HII phase made of one inverted cylinder (and waters inside) in a triclinic box with 90, 90, 60 angles. After running the simulation, this cylinder become bent like a curve. I.e. is not a perfect cylinder anymore. As a result, some water molecules and lipids pass the b

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 P

[gmx-users] PBC

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 PBC (periodic boundary condition) in

[gmx-users] PBC problem

Hello, I try to visualize a .gro file from Martini simulation. However, I noticed that the lipids always above the water molecule and my protein split into two. Even after I run the following command: gmx trjconv -s dppc-md.tpr -f dppc-md.gro -pbc whole -dump 0 -o dppc-md-pbc.gro The issue

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 t

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 do you think this is the n

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 co

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

Hi, it is not an issue !! To resolve your problem you could simulate two bilayer in box and insert the peptides between them. HTH -- Message: 6 Date: Wed, 9 Nov 2016 16:07:26 +0530 From: Abhi Acharya To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-us

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 20

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 somethin

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: > You could try to fit first

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 31 March 2016 at 05:45,

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 structure in nvt_water_fro

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 > On Mar 31, 2016 0

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 initial molecule is not frag

[gmx-users] -pbc nojump failure

Hi, I am simulating a protein in its unit cell. I use the original .pdb file as an input, so the initial molecule is not fragmented. At the end of the simulation, I generate a .pdb file containing the trajectory of the protein as follows: gmx trjconv -f nvt_water_frozen.trr -s nvt_water_frozen.

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 explanatio

[gmx-users] pbc

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? Regards Masrul -- Gromacs Users mailing list * Please search t

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 In

[gmx-users] pbc

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 Autumn -- Gromacs Users mailing list * Please

[gmx-users] pbc=xy with 2 walls and verlet scheme

Hi all, I use GROMACS 5.1. With pbc = xy nwall= 2 and cutoff-scheme = group everything runs fine, however, when I switch to cutoff-scheme = verlet the simulation crashes with a floating exception. Both cases can be downloaded here https:/

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 applied during simula

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 simulation. However in the

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,

[gmx-users] PBC in membrane protein system

Hi all, I am simulating a membrane protein in coarse-grained mode. The protein diffuse in the membrane and in the final frame my protein is in one of the box borders, so the coordinates are splitted to the opposite border (PBC). Then when I used backward.py to translate to all-atom coordinate

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 wrote: > Hi Mark, > Thank

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 gromacs? Is it right >

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 5,

[gmx-users] PBC

Dear users, If I dont define pbc=no, what is the default type for gromacs? Is it right if I dont use pbc=no in my system while using grid for ns-type? thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before post

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

Sent: Tuesday, August 4, 2015 1:59 PM To: Discussion list for GROMACS users Subject: 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 minimiz

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

[gmx-users] PBC in a closed box.

Hi all, I am trying to simulate the effusion process of water through hole in a very thin film. The film is partitioning the water box, I wish to count the numbers of waters before and after the simulation in each compartment, but I am afraid that the use of periodic boundary conditions will ma

Re: [gmx-users] PBC issue

x-users-boun...@maillist.sys.kth.se on behalf of tm651209 Sent: 03 July 2015 06:29 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] PBC issue Dear all, I pulled a protein using pdc=xyz, and want to do unloading simulation. The problem is both ends of the protein run out of

[gmx-users] PBC issue

Dear all, I pulled a protein using pdc=xyz, and want to do unloading simulation. The problem is both ends of the protein run out of the boundary after pulling. After unloading for a while, I found that both ends did not connect to where they should connect. Is there a way that I can regenerat

[gmx-users] PBC "no domain decomposition" error

Never mind my previous message. When I included periodicmolecule = yes in the mdp file, I believe that took care of the problem. Thanks, Jon - Hey! I ran into an issue when simulating graphene sheets with periodic boundary conditions. It said: The

Re: [gmx-users] PBC "no domain decomposition" error

It is my understanding that PBC will be (and really must be) taken into account whenever the bonds across the box are present in your topology and periodic-molecules is enabled in your mdp. Whether the particle population is now optimally decomposed to utilize the number of cores you've got is anot

[gmx-users] PBC "no domain decomposition" error

Hey! I ran into an issue when simulating graphene sheets with periodic boundary conditions. It said: There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 4.685 nm I figured that was due to the apparent bond length of the carbons connected

[gmx-users] pbc=z, applying pbc only along the z-direction

Hi Gromacs users, I have a confined system in both x and y directions. Gromacs offer 3 options for pbc=xyz or no or xy. Is there a way we can implement the pbc only along the z direction ? As I am using cutoff methods for electrostatistics one way to do this is to put some empty space (larger tha

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

[gmx-users] PBC problem in bilayer system

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 this tool (g_traj)? Is g_dist appropriate for

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 this

[gmx-users] PBC problem in bilayer system

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. My last question is that can I use this trajectory for doing analysis such as g_traj, g_dist, g_d

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 lip

[gmx-users] PBC problem in bilayer system

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 lipid bilayer (black line) as a function of simula

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 m

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: https://www.dropb

[gmx-users] PBC problem in bilayer system

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: https://www.dropbox.com/s/345o7lvc9z4jwln/figure%204.TIF?dl=0 --

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 (8.30034),

[gmx-users] PBC problem in bilayer system

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 (8.30034), for z. When I see **.xtc using vmd, problem w

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 sai

[gmx-users] PBC problem in bilayer system

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? -- Gromacs Users mailing list * Please search the archive at http

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 molecul

[gmx-users] PBC problem in bilayer system

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 molecules) are seen in other side of bilayer (bottom).

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

[gmx-users] PBC problem in bilayer system

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. please guide me to solve this problem as soon as possible. Best, -- Gromacs Users mailing list * Please search the

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

On 9/11/14 1:51 PM, shahab shariati wrote: Dear Justin Very thanks for your answer. Unfortunately, I am beginner in MD simulation of bilayer membrane systems. Based on your answer (You can try the translation options of trjconv in conjunction with -pbc mol), should I use following command?

[gmx-users] PBC problem in bilayer system

Dear Justin Very thanks for your answer. Unfortunately, I am beginner in MD simulation of bilayer membrane systems. Based on your answer (You can try the translation options of trjconv in conjunction with -pbc mol), should I use following command? trjconv –trans –pbc mol trjconv –pbc nojump

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. Is

[gmx-users] PBC problem in bilayer system

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. Is this state normal? -- Gromacs Users mailing l

[gmx-users] PBC problem in bilayer system

Dear Gromacs users Unfortunately, no one did not answer my previous question about selection of appropriate option for trjconv -pbc to solve pbc problem. For preparation of initial system, I inserted 4 drug molecules in close vicinity to the membrane surface in water phase, in one side of bilayer

[gmx-users] PBC problem in bilayer system

Dear Michael Carter Thanks for your answer. I used -pbc nojump Followed by -fit rot+trans Unfortunately, my problem was not solved. Please guide me to solve this problem. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_Lis

[gmx-users] PBC problem in bilayer system

Dear Michael Carter Thanks for your answer. I used -pbc nojump Followed by -fit rot+trans Unfortunately, my problem was not solved. Please guide me to solve this problem. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_Lis

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 problem in bilayer system

Hi, Try -pbc nojump Best, Mike On 09/09/2014 15:11, "shahab shariati" 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 the box. > >How t

[gmx-users] PBC problem in bilayer system

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 the box. How to resolve this PBC problem? which of -pbc options (none, mol, res, atom, nojump, cluster or

[gmx-users] PBC only on x and y in an NPT ensemble

Dear all I would like to simulate coarse grained thin polymer films supported on a wall or a substrate (I don't really mind) but with the one interface to be free. I would like to do this under NPT conditions. I would expect that this can only be done by putting pbc=xy, as in the to the following

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 trjco

[gmx-users] PBC problems??

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 trjconv -pbc mol, should stop the problem, but th

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 t

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

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 possibilities: 1. You built the system wrong and trjconv can't fix it. Without the full sequence of commands used to build the system, no one can p

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

Dear Mark, I’ve used numbers. Just indicated them as x_box/2, etc to be clearer. Juan C. > > 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 > > trjcon

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

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 the

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 th

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 https://www.dropbox.com/s/az1gvb299y6wh8h/Scr

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 typ

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

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 types of trjconv combinations with -pbc -ur or -fi

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