[gmx-users] pbc off

Hey everyone, If I ran my simulations with periodic boundary conditions, is there a way in Gromacs to get a trajectory file tracking the diffusion of the molecules in the first time frame (i.e. not allow them to exit one side of the box and reenter the other side)? If not, can I specify this in

Re: [gmx-users] pbc off

On 10/30/13 11:42 AM, jwill...@andrew.cmu.edu wrote: Hey everyone, If I ran my simulations with periodic boundary conditions, is there a way in Gromacs to get a trajectory file tracking the diffusion of the molecules in the first time frame (i.e. not allow them to exit one side of the box and

[gmx-users] pbc problem

Dear Mark Very thanks for your reply To make this clear, center the trajectory on the water and watch the time evolution in some visualization program. I did your suggestion (center the trajectory on the water). Again, drug molecule is in region (1)in some frames and is in region (4) in other

Re: [gmx-users] pbc problem

On Tue, Oct 29, 2013 at 5:02 PM, shahab shariati shahab.shari...@gmail.comwrote: Dear Mark Very thanks for your reply To make this clear, center the trajectory on the water and watch the time evolution in some visualization program. I did your suggestion (center the trajectory on the

Re: [gmx-users] pbc problem

On 10/29/13 12:02 PM, shahab shariati wrote: Dear Mark Very thanks for your reply To make this clear, center the trajectory on the water and watch the time evolution in some visualization program. I did your suggestion (center the trajectory on the water). Again, drug molecule is in

[gmx-users] pbc problem

Dear Justin I want to study translocation of drug molecule in lipid bilayer. My gro file after minimization is em2.gro. After NPT-MD simulation, I obtained npt.gro and 0.xtc files. When I see trajectory by vmd, there are some things abnormal. I guess there is pbc problem. I attached these 3

Re: [gmx-users] pbc problem

On 10/27/13 8:16 AM, shahab shariati wrote: Dear Justin I want to study translocation of drug molecule in lipid bilayer. My gro file after minimization is em2.gro. After NPT-MD simulation, I obtained npt.gro and 0.xtc files. When I see trajectory by vmd, there are some things abnormal. I

[gmx-users] pbc problem

Dear Justin Please check this trajectory file (1.xtc) being smaller than 0.xtc. https://www.dropbox.com/s/9qd2l37qyfqvpox/1.xtc -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at

[gmx-users] pbc problem

Dear Justin I attached images related to before (em2.gro) and after equilibration. https://www.dropbox.com/s/yjkyj5ycshvp20u/images.docx -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at

Re: [gmx-users] pbc problem

Hi Shahab, What about running trjconv -pbc mol with a .tpr as input file? Cheers, Tsjerk On Sun, Oct 27, 2013 at 3:24 PM, shahab shariati shahab.shari...@gmail.comwrote: Dear Justin I attached images related to before (em2.gro) and after equilibration.

[gmx-users] pbc problem

Dear Tsjerk Wassenaar Very very thanks for your reply. I used trjconv -pbc mol. pbc problem was solved only for lipid molecules. When I see new trajectory by vmd, there are some problesm about drug molecule. https://www.dropbox.com/s/xq4s6az17buhvb8/images-2.docx If I show my system as 4

Re: [gmx-users] pbc problem

On 10/27/13 12:05 PM, shahab shariati wrote: Dear Tsjerk Wassenaar Very very thanks for your reply. I used trjconv -pbc mol. pbc problem was solved only for lipid molecules. When I see new trajectory by vmd, there are some problesm about drug molecule.

[gmx-users] pbc problem

Dear jkrieger I used 2 times trjconv tool: 1) trjconv -f npt.xtc -s npt.tpr -n index.ndx -o 2npt.xtc -pbc nojump 2) trjconv -f 2npt.xtc -s npt.tpr -n index.ndx -o 3npt.xtc -pbc mol -center Dear Mark I selected all lipid atoms for centering. With my manner, pbc problem was solved just for

Re: [gmx-users] pbc problem

On Oct 24, 2013 8:10 AM, shahab shariati shahab.shari...@gmail.com wrote: Dear jkrieger I used 2 times trjconv tool: 1) trjconv -f npt.xtc -s npt.tpr -n index.ndx -o 2npt.xtc -pbc nojump 2) trjconv -f 2npt.xtc -s npt.tpr -n index.ndx -o 3npt.xtc -pbc mol -center Dear Mark I selected

[gmx-users] pbc problem

Dear Mark Thank for your reply. If I show my system as 4 regions, my system before equilibration is as fallows: region (1): water + drug region (2): top leaflet of bilayer region (3): bottom leaflet of bilayer region (4): water After equilibration, drug molecule exits region (1) and enters

Re: [gmx-users] pbc problem

On 10/24/13 10:57 AM, shahab shariati wrote: Dear Mark Thank for your reply. If I show my system as 4 regions, my system before equilibration is as fallows: region (1): water + drug region (2): top leaflet of bilayer region (3): bottom leaflet of bilayer region (4): water After

Re: [gmx-users] pbc problem

As Justin said, there is no actual division between region 1 and 4. Apparently you got the free diffusion you asked for! :-) Mark On Thu, Oct 24, 2013 at 4:57 PM, shahab shariati shahab.shari...@gmail.comwrote: Dear Mark Thank for your reply. If I show my system as 4 regions, my system

[gmx-users] pbc problem

Dear gromacs users My system contains DOPC + CHOLESTEROLO + WATER + drug molecules in a rectangular box. I put drug molecule in 2 position: a) drug in the center of bilayer membrane, b) drug inside water molecules in top leaflet. For both positions, I did energy minimization successfully with

Re: [gmx-users] pbc problem

I usually use -pbc nojump for my protein simulations and this works every time. Dear gromacs users My system contains DOPC + CHOLESTEROLO + WATER + drug molecules in a rectangular box. I put drug molecule in 2 position: a) drug in the center of bilayer membrane, b) drug inside water

Re: [gmx-users] pbc problem

Center on a particular lipid? Or head group? Mark On Oct 23, 2013 6:13 PM, shahab shariati shahab.shari...@gmail.com wrote: Dear gromacs users My system contains DOPC + CHOLESTEROLO + WATER + drug molecules in a rectangular box. I put drug molecule in 2 position: a) drug in the center of

[gmx-users] PBC problem

Hi all, I have a question about PBC. If I have a polymer chain that is longer than the box length, will the properties of the chain change because the tail of the chain may interact with the head of the chain due to PBC? Thank you! Yutian -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] PBC problem

Hi Yutian Yang, Yes. That is, if the chain is interacting with itself. If it remains curled up, then it won't be a problem. Cheers, Tsjerk On Thu, Jun 27, 2013 at 10:10 PM, Yutian Yang yyan...@syr.edu wrote: Hi all, I have a question about PBC. If I have a polymer chain that is longer

Re: [gmx-users] pbc problem

On 4/14/13 11:21 PM, Kieu Thu Nguyen wrote: Thank Justin ! I used the command editconf -center and i saw my membrane was in center of the box. I am stupid in that how putting the bilayer in a periodic image (instead between two periodic images as it was). Can you give me some instructions ?

Re: [gmx-users] pbc problem

Thank Justin ! I used the command editconf -center and i saw my membrane was in center of the box. I am stupid in that how putting the bilayer in a periodic image (instead between two periodic images as it was). Can you give me some instructions ? Many thanks ! On Fri, Apr 12, 2013 at 6:52 PM,

[gmx-users] pbc problem

Dear All, I made a POPC bilayer and carried out embedding a protein into this membrane. But the fatal error has appeared : Fatal error: Something is wrong with your membrane. Max and min z values are 12.342000 and 0.016000. Maybe your membrane is not centered in the box, but located at the box

Re: [gmx-users] pbc problem

On Fri, Apr 12, 2013 at 7:48 AM, Kieu Thu Nguyen kieuthu2...@gmail.comwrote: Dear All, I made a POPC bilayer and carried out embedding a protein into this membrane. But the fatal error has appeared : Fatal error: Something is wrong with your membrane. Max and min z values are 12.342000 and

[gmx-users] PBC for evaporation of droplets?

Dear all, I would like to ask you that using PBC for evaporation of droplets is necessary? Please note that the MD simulations are to be performed in vacuum. I checked the relevant references but in some of them PBC has been taken into account but in others not [for instance please see J.chem.

[gmx-users] PBC

Hello, I have question about periodic boundary condition. Suppose if one atom is going out of the box (x axis distance is more than L/2) and it will come inside the box from other side (distance-L). Distance before the pbc should be same or it will be different from center. Thanks Nilesh --

Re: [gmx-users] PBC

Hey Nilesh, Distance to where? Just think of your PBC in one dimension as being on a circle. Cheers, Tsjerk On Tue, Jun 26, 2012 at 4:26 PM, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: Hello, I have question about periodic boundary condition. Suppose if one atom is going out of the box (x

[gmx-users] PBC treatment: need an explanation

Dear gmx-users, I know that this is one of the most frequent subjects in the gmx-users list, however please let me ask you for a direct answer, since it seems to me that this particular question was not treated before. I'm performing MD simulations on a dimeric protein, using a rhombic

Re: [gmx-users] PBC treatment: need an explanation

On 4/24/12 6:51 AM, Anna Marabotti wrote: Dear gmx-users, I know that this is one of the most frequent subjects in the gmx-users list, however please let me ask you for a direct answer, since it seems to me that this particular question was not treated before. I'm performing MD simulations on

Re: [gmx-users] PBC treatment: need an explanation

Hi Anna, If there is a representation in which the units are together, then they're together. Trjconv can't put things together which are, in fact, separated. Cheers, Tsjerk On Tue, Apr 24, 2012 at 12:51 PM, Anna Marabotti anna.marabo...@isa.cnr.it wrote: Dear gmx-users, I know that this is

Re: [gmx-users] PBC - Protein and Ligands

Thank you all! That helped a lot! Steven On Wed, Feb 29, 2012 at 5:17 PM, Vedat Durmaz dur...@zib.de wrote: ** i always did it (successfully) with one single command: trjconv -f md.trr -s md.tpr -o mdCompact.trr -pbc mol -ur compact -n ../../index.ndx regards vedat Am 29.02.2012

Re: [gmx-users] PBC - Protein and Ligands

Steven Neumann wrote: Dear Gmx Users, I am run a simulation with Gromacs 4.5.4. of my protein and 15 ligands. The problem I face is PBC which I cannot get rid of. I used: 1. First make your molecules whole if you want them whole (system). trjconv -f md298SKIP4.xtc -s md298.tpr

Re: [gmx-users] PBC - Protein and Ligands

On 1 Mar, 2012, at 1:01, Steven Neumann s.neuman...@gmail.com wrote: Dear Gmx Users, I am run a simulation with Gromacs 4.5.4. of my protein and 15 ligands. The problem I face is PBC which I cannot get rid of. I used: 1. First make your molecules whole if you want them whole

Re: [gmx-users] PBC - Protein and Ligands

i always did it (successfully) with one single command: trjconv -f md.trr -s md.tpr -o mdCompact.trr -pbc mol -ur compact -n ../../index.ndx regards vedat Am 29.02.2012 18:01, schrieb Steven Neumann: Dear Gmx Users, I am run a simulation with Gromacs 4.5.4. of my protein and 15 ligands.

[gmx-users] pbc visualization advice

Hi all: I'm running a diffusion simulation involving a membrane protein and may be having a problem with the trjconv workflow. I have some molecules I'd like to study the diffusion of across the membrane (if it happens) and/or see if they interact with the membrane protein inside the membrane.

[gmx-users] -pbc nojump

Dear GROMACS users, I have a problem about trjconv -pbc nojump, I have 2 micelles in the end of my simulation. For analysis I should do three steps for micelle clustering at http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering?highlight=micelle+clustering  Steps 1 and 2 work good and

Re: [gmx-users] -pbc nojump

Hi Sara, The problem is that your micelle is formed at the end of the trajectory. To get what you want, you need to mirror the trajectory, follow the procedure you followed, and mirror the resulting trajectory. I posted a piece of python code for mirroring a trajectory a while back:

Re: [gmx-users] -pbc nojump

Hi Sara, Please keep discussions on the list. I'm not your private tutor. Whether you can do your analysis depends on the analysis you want to do. But if your aim is analyzing the formation of the micelle, you're probably better of reversing the trajectory. 1- trjconv -f md.trr -o md1.xtc -n

Re: [gmx-users] -pbc nojump

Thank you very much from your reply. Best Regards Sara From: Tsjerk Wassenaar tsje...@gmail.com To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, December 29, 2011 1:56 AM Subject: Re: [gmx-users] -pbc

[gmx-users] PBC - Protein - ligand

Dear Gmx Users, I know that this problem has been discussed may times but I cannot find the solution to get rid of pbc in my system: protein and ligand. I followed the workflow: 1. First make your molecules whole if you want them whole trjconv -f md.trr -s md.tpr -pbc whole -ur compact -o

Re: [gmx-users] PBC - Protein - ligand

Hi Steven, Don't use -ur compact in the first step and see if that solves the problem. Oh, and be sure that the thing is not just diffusing. There was a thread lately where a diffusing ligand drove someone mad trying to remove the 'jumps'. Cheers, Tsjerk On Mon, Nov 7, 2011 at 3:08 PM, Steven

Re: [gmx-users] PBC - Protein - ligand

Steven Neumann wrote: Dear Gmx Users, I know that this problem has been discussed may times but I cannot find the solution to get rid of pbc in my system: protein and ligand. I followed the workflow: 1. First make your molecules whole if you want them whole trjconv -f md.trr -s

Re: [gmx-users] PBC - Protein - ligand

On Mon, Nov 7, 2011 at 2:26 PM, Justin A. Lemkul jalem...@vt.edu wrote: Steven Neumann wrote: Dear Gmx Users, I know that this problem has been discussed may times but I cannot find the solution to get rid of pbc in my system: protein and ligand. I followed the workflow: 1. First

Re: [gmx-users] PBC - Protein - ligand

Hi Steven, Step 2: Cluster your molecules. This is where you have to forge a reference frame that you can use to remove jumps from your trajectory. If the ligand is not with the protein at the start, you'll have to shift it so that it is. Maybe -pbc cluster is your friend there. I do assume that

Re: [gmx-users] PBC - Protein - ligand

On 8/11/2011 3:17 AM, Steven Neumann wrote: On Mon, Nov 7, 2011 at 2:26 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: Dear Gmx Users, I know that this problem has been discussed may times but I cannot find the

[gmx-users] PBC

Hi everyone, In my .mdp MD file, I didn't put pbc =xyz. Then, I used tpbconv and mdrun to continue my simulation. My question is: did I run my simulation using periodic boundary conditions because I have the impression that I did but I'm not sure if not using the mention pbc in my mdp file

Re: [gmx-users] PBC

Carla Jamous wrote: Hi everyone, In my .mdp MD file, I didn't put pbc =xyz. Then, I used tpbconv and mdrun to continue my simulation. My question is: did I run my simulation using periodic boundary conditions because I have the impression that I did but I'm not sure if not using the

Re: [gmx-users] PBC

Thank you Justin, indeed it's pbc = xyz in my md.log file. Carla On Fri, Feb 25, 2011 at 3:20 PM, Justin A. Lemkul jalem...@vt.edu wrote: Carla Jamous wrote: Hi everyone, In my .mdp MD file, I didn't put pbc =xyz. Then, I used tpbconv and mdrun to continue my simulation. My question

Re: [gmx-users] -pbc nojump

On 20/10/2010 9:07 PM, leila karami wrote: Hi gromacs users I study simulation of protein-dna interaction using gromacs. After full md simulation, because of diffusion of one strand of dna to edge of box, I used trjconv -f old.xtc –o new.xtc –s *.tpr -pbc nojump -ur compact –center. By

[gmx-users] -pbc nojump

Dear Mark thanks for your attention when I used trjconv -pbc nojump, I made one group (protein and dna) in index file and I selected that as centering group. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] -pbc nojump

On 20/10/2010 9:24 PM, leila karami wrote: Dear Mark thanks for your attention when I used trjconv -pbc nojump, I made one group (protein and dna) in index file and I selected that as centering group. What is the problem? :-) You might need two passes with trjconv. Mark -- gmx-users

[gmx-users] -pbc nojump

Dear Mark my mean of [when I used trjconv -pbc nojump, I made one group (protein and dna) in index file and I selected that as centering group.] is that the problem (nonentity of water molecules in interface of protein and dna) was not solved. what is your mean of [You might need two passes with

Re: [gmx-users] -pbc nojump

On 20/10/2010 9:55 PM, leila karami wrote: Dear Mark my mean of [when I used trjconv -pbc nojump, I made one group (protein and dna) in index file and I selected that as centering group.] is that the problem (nonentity of water molecules in interface of protein and dna) was not solved. what

[gmx-users] -pbc nojump

Dear Mark you said in answer to -pbc nojump that using of new xtc file for analysis section depends what one wants to observe. what observations is relevant to periodicity? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

Re: [gmx-users] -pbc nojump

On 20/10/2010 10:26 PM, shahab shariati wrote: Dear Mark you said in answer to -pbc nojump that using of new xtc file for analysis section depends what one wants to observe. what observations is relevant to periodicity? Anything that measures where something is relative to another.

[gmx-users] pbc in one direction only for analysis?

Dear gromacs users I have surface groups anchored on a cylindrical pore wall (similar to a carbon nanotube). The pore runs along the z direction. I am trying to determine to what extent my surface groups are clustered together and was thinking of using g_mindist and/or g_rdf for this

[gmx-users] pbc in one direction only for analysis?

It's a messy solution, but you could 1. run trjconv so that your cylinder is in the unit cell 2. convert your trajectory to .gro files 3. massively expand the x and y dimensions of each .gro 4. join the .gros to a .xtc 5. g_rdf You could also use template.c to write a program that does this

[gmx-users] pbc atom

Gavin, I recall mentioning gen_vel=no with temperature coupling as a possible problem a while ago (the problem is that the initial forces become initial velocities and then those get scaled up and what you have are velocities and not temperatures -- read about the flying ice cube problem).

Re: [gmx-users] pbc atom

O.K Chris Thanks for all your help. I am actually considering removing the thermostat all together seeing as my system is quite small. I have also started using gen_vel = yes (no matter how much I think my system is in equilibrium). One quick question (perhaps its silly). When you say the initial

[gmx-users] pbc atom

velocities are not taken from the .gro as far as I know. You can get them from the .trr if you also use a .edr. If you want to check, then do a run for only 1 ps and save your .edr every timestep. Then run g_energy and look at the temperature. I am not sure that a constant energy

Re: [gmx-users] pbc atom

Dear Chris and Justin I ran a simulation for two water molecules (100 ns). It only took 5 minutes. Firstly I ran the simulation with ref distance 2.35 nm, genvel =yes, and gen temp =600 (using Nose Hoover). This produced a histogram with one main peak. I then took the final configuration from

[gmx-users] pbc atom

Hi all I am generating a series of configurations using the pull code to calculate the pmf. I am using no pbc i.e. pbc =no, howver the output from grommp gives me info on pbc atom. Pull group natoms pbc atom distance at start reference at t=0 07236 1

Re: [gmx-users] pbc atom

Gavin Melaugh wrote: Hi all I am generating a series of configurations using the pull code to calculate the pmf. I am using no pbc i.e. pbc =no, howver the output from grommp gives me info on pbc atom. Pull group natoms pbc atom distance at start reference at t=0 072

Re: [gmx-users] pbc atom

Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi all I am generating a series of configurations using the pull code to calculate the pmf. I am using no pbc i.e. pbc =no, howver the output from grommp gives me info on pbc atom. Pull group natoms pbc atom distance at start reference

Re: [gmx-users] pbc atom

Thanks Justin Have you any idea why when generating umbrella histograms for the pmf I would get two peaks in the histograms above a distance of 2 nm, but below 2 nm I get well behaved histograms that lead to a very good profile in the pmf. To the best of my knowledge the configurations are all

Re: [gmx-users] pbc atom

Gavin Melaugh wrote: Thanks Justin Have you any idea why when generating umbrella histograms for the pmf I would get two peaks in the histograms above a distance of 2 nm, but below 2 nm I get well behaved histograms that lead to a very good profile in the pmf. To the best of my knowledge the

Re: [gmx-users] pbc atom

Gavin Melaugh wrote: O.K thanks anyway I saw the plots you posted during a conversation with Chris, but I'll ask the obvious anyway: have you watched the trajectories for any of the problematic windows? It didn't seem like you had two metastable states, but maybe having a look at the

Re: [gmx-users] pbc atom

Justin I have looked at the movies but it's very hard to tell what's going on as I save teh trajectories every 25 steps for every 5000 step simulation (100 ns). Ill look at them again in more detail and post back. Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: O.K thanks anyway

Re: [gmx-users] pbc atom

Gavin Melaugh wrote: Justin I have looked at the movies but it's very hard to tell what's going on as I save teh trajectories every 25 steps for every 5000 step simulation (100 ns). Ill look at them again in more detail and post back. Plotting the pullx.xvg file(s) may be useful,

Re: [gmx-users] pbc atom

I always used g_dist to plot the COM distances because the pullx.xvg files doesn't give this value directly. Can you access the COM distance from the pullx.xvg file Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Justin I have looked at the movies but it's very hard to tell what's going

Re: [gmx-users] pbc atom

Gavin Melaugh wrote: I always used g_dist to plot the COM distances because the pullx.xvg files doesn't give this value directly. Can you access the COM distance from the pullx.xvg file That's what is in pullx.xvg - coordinate (X,Y,Z) of the reference group, then displacement (dX,dY,dZ) of

Re: [gmx-users] pbc atom

For the umbrella sampling I am not pulling in any direction I am just applying the umbrella potential so that two molecules can sample space about a give value of r0 (COM distance). Maybe I am confused but should I not plot the absolute value of the displacement (modulus) as supposed to the

Re: [gmx-users] pbc atom

Gavin Melaugh wrote: For the umbrella sampling I am not pulling in any direction I am just applying the umbrella potential so that two molecules can sample space about a give value of r0 (COM distance). Maybe I am confused but should I not plot the absolute value of the displacement (modulus)

Re: [gmx-users] pbc atom

O.K thanks Justine I'll look at these files and see if there is any weirdness. Just to make sure that there are no cut-off artefacts. If I set the cut-offs to zero as in the following mdp file; that does mean that I am considering all electrostatic and LJ interactions between the molecules? and

Re: [gmx-users] pbc atom

Gavin Melaugh wrote: O.K thanks Justine I'll look at these files and see if there is any weirdness. Just to make sure that there are no cut-off artefacts. If I set the cut-offs to zero as in the following mdp file; that does mean that I am considering all electrostatic and LJ interactions

[gmx-users] pbc atom

I have seen this before, and there are a few possible reasons, but I'm still waiting to see that histogram with two peaks (http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html). It's really hard to help you when we have to guess what the problem looks like... or perhaps you

Re: [gmx-users] pbc atom

chris.ne...@utoronto.ca wrote: I have seen this before, and there are a few possible reasons, but I'm still waiting to see that histogram with two peaks (http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html). It's really hard to help you when we have to guess what the problem

Re: [gmx-users] pbc atom

Hi Chris Yeah I posted the histograms a few days ago as Justin said. Did you get the link? Gavin chris.ne...@utoronto.ca wrote: I have seen this before, and there are a few possible reasons, but I'm still waiting to see that histogram with two peaks

Re: [gmx-users] pbc atom

Justin In regard to my query regarding the cut-offs at zero with no pbc. I assume its is fine to have box dimensions (0 0 0) to comply with the definition of a vacuum simulation. I am just worried that there may be some default cut-off that I am not aware of. Cheers P.S I have plotted the

Re: [gmx-users] pbc atom

Gavin Melaugh wrote: Justin In regard to my query regarding the cut-offs at zero with no pbc. I assume its is fine to have box dimensions (0 0 0) to comply with the definition of a vacuum simulation. I am just worried that there may be some default cut-off that I am not aware of. You have

Re: [gmx-users] pbc atom

O.K Thanks My apologies for not stating earlier that I had the box dimensions set to zero but I thought that when you set pbc = no and ns_type = simple that ignore the box (from manual) was implemented. Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Justin In regard to my query

[gmx-users] pbc atom

you can post a step by step from the beginning where you copy and paste absolutely all of your commands (e.g. paste the *exact* grompp, mdrun, g_dist, etc. commands) and the complete .mdp file and the last line in your starting .gro file. Chris. -- original message -- [gmx-users] pbc atom

Re: [gmx-users] pbc atom

Gavin Melaugh wrote: O.K Thanks My apologies for not stating earlier that I had the box dimensions set to zero but I thought that when you set pbc = no and ns_type = simple that ignore the box (from manual) was implemented. Indeed. How many atoms are in your system? How well-conserved is

Re: [gmx-users] pbc atom

There are 168 atom types in my system, 2 molecules comprising of 84 atoms each. The average temperature is 600 K but there are large fluctuations ca ~100 K, which I assume is expected with such a smal system. Ill check the energies Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: O.K

Re: [gmx-users] pbc atom

all of your commands (e.g. paste the *exact* grompp, mdrun, g_dist, etc. commands) and the complete .mdp file and the last line in your starting .gro file. Chris. -- original message -- [gmx-users] pbc atom Gavin Melaugh gmelaugh01 at qub.ac.uk Tue Aug 24 17:19:45 CEST 2010 * Previous

Re: [gmx-users] pbc atom

message -- [gmx-users] pbc atom Gavin Melaugh gmelaugh01 at qub.ac.uk Tue Aug 24 17:19:45 CEST 2010 * Previous message: [gmx-users] pbc atom * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] Hi Chris Yeah I posted the histograms a few days ago as Justin said. Did

[gmx-users] pbc atom

Dear Gavin: What happens if you replace your reference group by a single water molecule and your pulled group by a single water molecule and run the 2.35 nm simulation again. Do you get the same two-peaked histogram? What about if you use a system with a single water for the reference

Re: [gmx-users] pbc atom

Gavin Melaugh wrote: There are 168 atom types in my system, 2 molecules comprising of 84 atoms each. The average temperature is 600 K but there are large fluctuations ca ~100 K, which I assume is expected with such a smal system. Ill check the energies I would think it possible, even

Re: [gmx-users] pbc atom

Hey, directly. I think you want this (assuming that cols 5,6,7 give you the dx,dy,dz, which I believe that they do): cat pullx.xvg | grep -v '[#|@]' | awk '{print $1,sqrt($5*$5+$6*$6+$7*$7)}' my.data Nothing directly harmful of course, but why using three programs for this? awk will do

[gmx-users] pbc atom

Tsjerk, Two reasons. First, I simply don't understand awk as well as you do. Second, I think that breaking it down into simpler commands linked by pipes is better for teaching. If somebody needs help to combine 3 cols into a vector distance, then they may copy and paste your solution to

[gmx-users] PBC

Morteza Khabiri wrote: Dear users I have a dimer protein in the water box. It was run for 30ns. during the simulation dimer split to two monomer. This things happen bc of PBC. ( I checked it by vmd pbc option ) to have a two monomer together during trajectories (for visualization) I have

Re: [gmx-users] PBC

Hi Morteza, I had this problem when I was running a trimeric protein attached to an oligosaccharide. *I have used the following command:* * * *trjconv -s .tpr -f .xtc -o -boxcenter tric -pbc mol* * * *but it is not working.* Do the following. It worked for me. In the first round, run

[gmx-users] PBC

Dear users I have a dimer protein in the water box. It was run for 30ns. during the simulation dimer split to two monomer. This things happen bc of PBC. ( I checked it by vmd pbc option ) to have a two monomer together during trajectories (for visualization) I have used the following command:

Re: [gmx-users] PBC

On 02/06/10 18:48, Morteza Khabiri wrote: Dear users I have a dimer protein in the water box. It was run for 30ns. during the simulation dimer split to two monomer. This things happen bc of PBC. ( I checked it by vmd pbc option ) to have a two monomer together during trajectories (for

Re: [gmx-users] pbc whole

Hi, Actually, the ligand I'm using is an ATP molecule, and from the beginning, ATP is not bound to my protein by a chemical bond. It is just crystallized with my protein. I checked with genconf now I'm certain that my ATP molecule is still with the protein, but why trjconv doesn't work why I

Re: [gmx-users] pbc whole

Hi Carla, I checked with genconf now I'm certain that my ATP molecule is still with the protein That's good to know :) trjconv -s a.tpr -f b.xtc -o c.xtc -center -ur compact -pbc mol (centering on Protein) So what did come out of this then? It should have given you a compact

Re: [gmx-users] pbc whole

Hi Tsjerk, sorry I didn't understand this part of your explanation:Can you make an image of the last frame and send a link to it? But anyhow, please can you send me the version of trjconv that does the trick? Thanks, Carla On Thu, Feb 18, 2010 at 11:42 AM, Tsjerk Wassenaar

Re: [gmx-users] pbc whole

Carla Jamous wrote: Hi Tsjerk, sorry I didn't understand this part of your explanation:Can you make an image of the last frame and send a link to it? Render an image of your system from the end of your trajectory and post it somewhere online (like photobucket); do not send it as an

  1   2   >