Re: [gmx-users] how to visualize gromacs trajectory

Hi, Yes that command is right. If you need to do other commands, the trjconv description and options are in the second link I gave: http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-trjconv.html Regards, Stephani On Tue, 9 Jul 2019 at 00:13, sunyeping wrote: > Hello, steph, > > I

Re: [gmx-users] how to visualize gromacs trajectory

Hello, It sounds like you have to fixed broken molecules and have problem with boundary conditions. After doing the MD, you need to fix your trajectory first before doing visualization. Check this link for a workflow: http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

[gmx-users] NPT equilibration fatal error

Hello, I am equilibrating a protein ligand system in a bilayer membrane and I receive this error for my 5th equibiration (4th NPT) Fatal error: 5 particles communicated to PME rank 0 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.

[gmx-users] equilibration error

Hello, I am planing to do MD of a membrane protein bound to a ligand. I already have my files and I am doing my 6 step equilibration with reducing force constants. However, in the 5th step, it gave an error saying that the previous system (4th step) was not well equilibrated: Fatal error: 5

Re: [gmx-users] bilayer thickness 100ns membrane protein

in your protein? How you > made the topology file after preparing the system in CHARMM-gui > > On Tue, Sep 18, 2018, 12:25 PM Stephani Macalino < > stephanimacal...@gmail.com> > wrote: > > > Hi Bratin, > > Sorry, I can't advise you on this. I am a newbie in this fi

Re: [gmx-users] bilayer thickness 100ns membrane protein

.in> wrote: > Dear Stephani, > I tried charmm-gui to pack the lipid bilayer > arround my protein. But charmm gui is giving fatal error. what possible > reason can be there for this fatal error. > > On Tue, Sep 18, 2018 at 11:01 AM, Stephani Macalino < &

Re: [gmx-users] bilayer thickness 100ns membrane protein

same > tutorial explained by justin lemkul > > On Sun, Sep 16, 2018 at 9:46 PM, Stephani Macalino < > stephanimacal...@gmail.com> wrote: > > > Hello, > > I ran a 100ns MD or a membrane protein and am now analyzing the APL and > > bilayer thickness from the trajector

Re: [gmx-users] bilayer thickness 100ns membrane protein

at around 40. After I use -pbc mol - center, the strange value jumps are observed. I want to know if it is okay to just leave off the mol center? Hope you can help. Thank you! Regards, Stephani On Mon, 17 Sep 2018 at 06:47, Stephani Macalino wrote: > Hello, > Thanks for the response. But

Re: [gmx-users] bilayer thickness 100ns membrane protein

n 9/16/18 12:16 PM, Stephani Macalino wrote: > > Hello, > > I ran a 100ns MD or a membrane protein and am now analyzing the APL and > > bilayer thickness from the trajectory file of 50,000 frames. > > When I graphed the values, around 20 to 30k frames in (and some frames >

[gmx-users] bilayer thickness 100ns membrane protein

Hello, I ran a 100ns MD or a membrane protein and am now analyzing the APL and bilayer thickness from the trajectory file of 50,000 frames. When I graphed the values, around 20 to 30k frames in (and some frames along 40k) the value jumps from 40 to 70. The rest of the frames have pretty similar

Re: [gmx-users] Combining edr files for NPT with different dt values

't bother with any of > this for equilibration. If the last segment is consistent with the ensemble > you seek, then that is the job done. > > Mark > > On Mon, Sep 3, 2018 at 2:11 AM Stephani Macalino < > stephanimacal...@gmail.com> > wrote: > > > Hello, > >

[gmx-users] Combining edr files for NPT with different dt values

Hello, I am trying to combine edr files using the gmx eneconv command. I did 6 cycles of equilibration (1 NVT and 5 NPT). The NPT cycles are 2ns each but the first 2 have a dt of 0.001 while the last 4 have dt of 0.002. I tried to combine them and check the density using gmx energy command but I