[gmx-users] Constraints between multiple molecules

Hi everyone.  I'm doing a simulation of a protein aggregate with 3 proteins.   Ideally, I would like to constrain the distance between the center of mass of peptide 1 and the COM of peptide 2, and also constrain the distance between the combined COM of peptides 1 & 2, with the COM of peptide 3.  

[gmx-users] Can gromacs automatically divided trajectory file into several parts during the simulation process?

Dear all, I am now try to do a long-time all atom simulation. The trajectory file is expected to be larger than 20G bytes. However, my simulation is run on a cluster which only allows me to store 5G bytes file. Therefore, I attempt to divided the trajectory file into several parts but not interrup

Re: [gmx-users] Problem in pullx file

Aswathy wrote: On Wed, Aug 4, 2010 at 4:31 PM, Justin A. Lemkul > wrote: Aswathy wrote: Dear Gromacs users, I am doing SMD of a ligand pathway, and then want ot do the PMF analysis. Initially I pulled the ligand from extra to i

Re: [gmx-users] Can gromacs automatically divided trajectory file into several parts during the simulation process?

张春雷 wrote: Dear all, I am now try to do a long-time all atom simulation. The trajectory file is expected to be larger than 20G bytes. However, my simulation is run on a cluster which only allows me to store 5G bytes file. Therefore, I attempt to divided the trajectory file into several part

[gmx-users] Re: Constraints between multiple molecules

One thing which you could do is to write your three proteins into one molecule definition (if you use .itp files, then make one .itp for all three). Then at the end of the molecule definition you can add the constraints. To merge the three proteins is rather easy but cumbersome, you must shift

Re: [gmx-users] Re: Constraints between multiple molecules

Thomas Schlesier wrote: One thing which you could do is to write your three proteins into one molecule definition (if you use .itp files, then make one .itp for all three). Then at the end of the molecule definition you can add the constraints. To merge the three proteins is rather easy but c

Re: [gmx-users] Problem in pullx file

Let me explain. Consider the channel of a membrane protein, r57 is a residue at the extracellular loop in this channel. I docked my ligand to the start of the channel. ie; just below the r57. (Here the I have not started from the solvent, but at the mouth of the channel , just below r 57..) Then

Re: [gmx-users] Problem in pullx file

Aswathy wrote: Let me explain. Consider the channel of a membrane protein, r57 is a residue at the extracellular loop in this channel. I docked my ligand to the start of the channel. ie; just below the r57. (Here the I have not started from the solvent, but at the mouth of the channel , ju

[gmx-users] linear molecules

Hi, I want to simulate a system of linear molecules like CO2 with periodic boundary conditions. I think this can be done with the virtual sites algorithm. I have started with GROMACS today. Do you have some sample scripts for linear molecules which use the virtual site algorithm which could hel

[gmx-users] abnormal stop of job

Hi all, I have been running a simulation of 200 ns length and it suddenly stoped at 67 ns showing the following line - Received the TERM signal, stopping at the next step I have checked the time steps properly and there is no error. What should I do now? Please suggest. Thanks Samr

Re: [gmx-users] linear molecules

nadia teresa de la cruz canul perez wrote: Hi, I want to simulate a system of linear molecules like CO2 with periodic boundary conditions. I think this can be done with the virtual sites algorithm. I have started with GROMACS today. Do you have some sample scripts for linear molecules which

[gmx-users] new beta release - gromacs-4.5-beta2

Since the charmm force field has some instances with large charge groups (grompp warns you for it) it is advisable to use a longer cut-off (or no cut-off at all, by setting them all to 0). I've run 200 ns simulations with 1.5 nm and nstlist = 5 and a timestep of 2 fs and constraints = all-b

Re: [gmx-users] new beta release - gromacs-4.5-beta2

Hi! Is this with GBSA implicit solvent, and in that case what Born radii model? Could you mail me the tpr off-list, and I'll have a look at it. Cheers /Per 5 aug 2010 kl. 20.26 skrev Elio Cino: > > Since the charmm force field has some instances with large charge groups > (grompp warns yo

Re: [gmx-users] abnormal stop of job

On Thu, Aug 5, 2010 at 1:37 PM, Samrat Pal wrote: > > Received the TERM signal, stopping at the next step The TERM signal is the default signal sent by the command "kill" to stop a job. Pressing Ctrl-C while the program is running on the foreground has the same effect. -- Elton Carvalho Tel.: +