Re: [gmx-users] cant load trajectory, low memory

Hi, I'm facing a strange problem. I have equilibrated my protein-ligand system in NVT run of 20ns. The temperature curve get finely converged here. But when I try to run NPT after that, it gives me an issue as "The sum of the two largest charge group radii (13.169886) is larger than rlist

Re: [gmx-users] cant load trajectory, low memory

Hi, Presumably that was discussed in the tutorial you were following. The Unix diff tool can help with physically inspecting what is different between those files. But really you should already know! A good rule of thumb is not run a big calculation on expensive hardware unless you know why you

Re: [gmx-users] cant load trajectory, low memory

Hi, I'm going with it. I still have a question. If I reconstruct the system (stripping the solvent and thus making smaller box size) I need to go through NVT>NPT equilibrations again. This part I got it. The question is, do I need to run the npt_umbrella.mdp or simple npt.mdp will do ? What is

Re: [gmx-users] cant load trajectory, low memory

On 4/24/17 12:56 PM, abhisek Mondal wrote: Hello, I'm using the configurations generated by pulling run to re-box > resolvate ion addition > EM > npt_umbrella(10ns) and forward. So, please clarify me something. Am I following correct path ? Should I have given a npt equilibration step

Re: [gmx-users] cant load trajectory, low memory

Hello, I'm using the configurations generated by pulling run to re-box > resolvate > ion addition > EM > npt_umbrella(10ns) and forward. So, please clarify me something. Am I following correct path ? Should I have given a npt equilibration step prior to npt_umbrella step ? Thank you. On Mon,

Re: [gmx-users] cant load trajectory, low memory

Hi, I already answered that. You're effectively starting again, so do that. Mark On Mon, Apr 24, 2017 at 12:28 PM abhisek Mondal wrote: > Ok, I got it this time. > But what kind of equilibration I'm to perform on these stripped structures. > Should I perform normal NPT

Re: [gmx-users] cant load trajectory, low memory

Ok, I got it this time. But what kind of equilibration I'm to perform on these stripped structures. Should I perform normal NPT equilibration as done before generating configurations ? or I'm to run gmx grompp -f npt_umbrella.mdp -c conf0.gro -p topol.top -n index.ndx -o npt0.tpr (using standard

Re: [gmx-users] cant load trajectory, low memory

If you are taking confout.gro as your starting input file, it will have all water and ions of the previous simulation. On Mon, Apr 24, 2017 at 3:35 PM, Tasneem Kausar wrote: > Create index group that have both protein and ACO. gmx make_ndx will serve > this task. >

Re: [gmx-users] cant load trajectory, low memory

Create index group that have both protein and ACO. gmx make_ndx will serve this task. Then create a pdb file file from gmx trjconv Or you can choose system as output and delete ions and solvent from any editor. On Mon, Apr 24, 2017 at 3:21 PM, abhisek Mondal wrote: >

Re: [gmx-users] cant load trajectory, low memory

Hi, You need to make an index group (e.g. gmx select or gmx make_ndx) that has the things you want (e.g. protein + ACO, or perhaps everything but water+ions). See also http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume. I'd guess your system has at least a factor of

Re: [gmx-users] cant load trajectory, low memory

Hello, Alright. I have tried this but I'm stuck in the following scenario. I'm using trjconv for getting pdb file of the protein-ligand complex (used for umbrella sampling). trjconv_mpi -f confout1.gro -o conf_1.pdb -n index.ndx -s npt.tpr This is giving me the following prompt: Select group for

Re: [gmx-users] cant load trajectory, low memory

Hi, Take a configuration of interest, strip the solvent, put it in a box you think is good, and re-equilibrate just like you did before you started. Mark On Sun, Apr 23, 2017 at 8:59 PM abhisek Mondal wrote: > Hi, > > Yes, I did when I started the simulation. The box

Re: [gmx-users] cant load trajectory, low memory

Hi, Yes, I did when I started the simulation. The box size I used to start the simulation was very big(I was dealing with an unknown sample). After successfully generating the configurations I realized that further work could move faster if I could trim the box size little bit now. So is there

Re: [gmx-users] cant load trajectory, low memory

Hi, You get to choose the box size eg with editconf when you set up your simulation. It's not pre-defined ;-) Mark On Sun, 23 Apr 2017 20:28 abhisek Mondal wrote: > Hello, > > Another thing I wanted to ask. > After generating configurations I found out that the

Re: [gmx-users] cant load trajectory, low memory

Hello, Another thing I wanted to ask. After generating configurations I found out that the predefined box size (used to reach so far) is excessively high. Is it possible to trim the box size to perform further mdrun during umbrella sampling? Please suggest me a way, it is taking very long time

Re: [gmx-users] cant load trajectory, low memory

Hi, You can only load a trajectory with fewer frames. Either don't write so many, or filter it with trjconv first. Mark On Sun, 23 Apr 2017 17:20 abhisek Mondal wrote: > Hi, > I'm having a problem loading trajectory file after umbrella sampling. The > file is so huge

[gmx-users] cant load trajectory, low memory

Hi, I'm having a problem loading trajectory file after umbrella sampling. The file is so huge in size that the VMD finally runs out of memory. I'm operating with 125gb of physical memory here though. Is there any way out of it ? Thank you -- Abhisek Mondal *Senior Research Fellow*