Re: [gmx-users] local pressure calcuation for Gromacs-4.5

Dear all, I have made a test calculation of local pressure using version 4.5 for my membrane simulation using CHARMM FF. When rerun the simulation, mdrun gives the localpressure data. Howeve, instead of giving an anveraged data of the local pressure, mdrun gives a separate file for each frame,

Re: [gmx-users] local pressure calcuation for Gromacs-4.5

On 15/06/2011 9:09 PM, Jianguo Li wrote: Dear all, I have made a test calculation of local pressure using version 4.5 for my membrane simulation using CHARMM FF. When rerun the simulation, mdrun gives the localpressure data. Howeve, instead of giving an anveraged data of the local pressure, m

Re: [gmx-users] Questions about GB parameters

On 15/06/2011 4:24 AM, Justin A. Lemkul wrote: Hi All, I wanted to dig up an old discussion that hit the list a long time ago because I'm now encountering some problems understanding the GB settings myself. The discussion in question is here: http://lists.gromacs.org/pipermail/gmx-users/20

Re: [gmx-users] Water Potential Energy

On 15/06/2011 4:55 AM, Rini Gupta wrote: Dear Mark, Thanks for the reply! I am using the same NPT conditions except time constants. The simulation was performed at constant temperature (300K) and pressure(1 bar) using velocity rescaling algorithm (tau=0.1 ps) for temperature coupling and Berend

[gmx-users] trjcat crashes with error 9360 killed when concatenating large number of frames, bug ?

I am using the command: trjcat -f *gro -o temp.xtc -cat to concatenate about 40,000 frames of 14,000 atoms each. The commands works well for 10,000 frames, but crashes for 40,000 frames after reading all the frames. There is sufficient disk space. Is this a bug of some kind? -- Maria G. Technic

Re: [gmx-users] trjcat crashes with error 9360 killed when concatenating large number of frames, bug ?

On 15/06/2011 10:58 PM, maria goranovic wrote: I am using the command: trjcat -f *gro -o temp.xtc -cat to concatenate about 40,000 frames of 14,000 atoms each. The commands works well for 10,000 frames, but crashes for 40,000 frames after reading all the frames. There is sufficient disk space

Re: [gmx-users] trjcat crashes with error 9360 killed when concatenating large number of frames, bug ?

maria goranovic wrote: I am using the command: trjcat -f *gro -o temp.xtc -cat to concatenate about 40,000 frames of 14,000 atoms each. The commands works well for 10,000 frames, but crashes for 40,000 frames after reading all the frames. There is sufficient disk space. Is this a bug of s

Re: [gmx-users] trjcat crashes with error 9360 killed when concatenating large number of frames, bug ?

thanks for the help .. will try On Wed, Jun 15, 2011 at 3:02 PM, Justin A. Lemkul wrote: > > > maria goranovic wrote: > >> I am using the command: >> >> trjcat -f *gro -o temp.xtc -cat >> to concatenate about 40,000 frames of 14,000 atoms each. The commands >> works well for 10,000 frames, but c

[gmx-users] initial temperature ridiculously high

Hi, ALL I met a bizarre in a NVT simulation in which the initial temperature is ridiculously high. Even though I specify the initial temperature to be 200 K. ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen_temp = 200.0 gen_seed = 173529 En

Re: [gmx-users] initial temperature ridiculously high

GZ Zhang wrote: Hi, ALL I met a bizarre in a NVT simulation in which the initial temperature is ridiculously high. Even though I specify the initial temperature to be 200 K. ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen_temp = 200.0 gen_seed

Re: [gmx-users] Regarding H-bond autocorrelation

Thanks Sir,for your reply... I have a silly question regarding the g_hbond's autocorrelation output: The output contains the following four columns (i) Ac fin sys(t) (ii) Ac(t) (iii) Cc contact,hb(t) (iv) -dAc fs/dt As I understood the first column is the acf with background subtraction,and the

Re: [gmx-users] Reducing density using -vdwd option for a new solvent in the system

Hello Justin and everybody, I created a system of charged polyhistdine, counter anions and just 1 DHB molecule is a box without making any change in the vdwradii.dat file. This system does not energy minimize, it stops with the same message: Stepsize too small, or no change in energy. Converged t

Re: [gmx-users] Reducing density using -vdwd option for a new solvent in the system

shivangi nangia wrote: Hello Justin and everybody, I created a system of charged polyhistdine, counter anions and just 1 DHB molecule is a box without making any change in the vdwradii.dat file. This system does not energy minimize, it stops with the same message: Stepsize too small, or no

[gmx-users] centering a bilayer at a cartesian coordinate

Dear users: I am trying to process a trajectory so that a group of molecules has their center of mass at a constant position in Cartesian space. I have not been able to figure out how to do this. The reason that I would like this is that I have conducted umbrella sampling of a solute alon

[gmx-users] centering a bilayer at a cartesian coordinate

I solved it. It was my own error to assume that trjconv -center centers the COM. Actually, it centers the value of (min+max)/2 in each dimension. I can modify trjconv locally to do what I want. Thank you, Chris. static void center_x(int ecenter,rvec x[],matrix box,int n,int nc,atom_id ci[

[gmx-users] CHARMM forcefield

Hi, I have two questions about using the charmm force field. 1. Do we still need to use the two perl scripts, convert_charmm_ to_gromacs.pl and fix_top_for_charmm.pl? 2. I got the following note when I tried to do energy minim. with grompp: NOTE 1 [file topol.top]:   The largest charge group con

Re: [gmx-users] local pressure calcuation for Gromacs-4.5

Dear all, Could anyone direct me to the manual for local pressure calculation or a place where everything is mentioned about it ? I have been only able to collect bits and pieces from the mailing lists. Thank you Amit On Wed, Jun 15, 2011 at 5:35 AM, Mark Abraham wrote: > On 15/06/2011 9:09 PM

Re: [gmx-users] CHARMM forcefield

simon sham wrote: Hi, I have two questions about using the charmm force field. 1. Do we still need to use the two perl scripts, convert_charmm_ to_gromacs.pl and fix_top_for_charmm.pl? No. 2. I got the following note when I tried to do energy minim. with grompp: NOTE 1 [file topol.top]:

Re: [gmx-users] local pressure calcuation for Gromacs-4.5

Amit Choubey wrote: Dear all, Could anyone direct me to the manual for local pressure calculation or a place where everything is mentioned about it ? I have been only able to collect bits and pieces from the mailing lists. That's probably all there is to be found. There's no manual link

[gmx-users] Including quadrupole-charge interaction in GROMACS

Dear GMXers, Is there a way in GROMACS to include quadrupole-charge interaction? Or is there a standard to way to mimic quadrupole moment using partial charge? Thank you. Best, Yanbin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please s

[gmx-users] g_density

Dear Matthias: Did you run trjconv -center -pbc mol at some point before running g_density? With pbc, there are multiple ways to put the center of a system at the center of the box. This can lead to having the water slab in the center of the unit cell and the bilayer on the top and bottom

[gmx-users] Position restraints

Greetings all, I have run into a little bit of a problem. I am trying to simulate a hetro-dimer. Through previous work we have identified 302 C-alphas (of 960 odd residues) that don't move much. Previously we position restrained these atoms in our simulations using charmm which gave us a sign