Re: [gmx-users] Not enough memory. Failed to calloc :

You don't have enough memory ;-) get more, or do a smaller task Mark On Thu, 21 Jan 2016 11:51 Nikhil Maroli wrote: > Dear all, > i was trying run g_mmpbsa for trajectory of 100ns protein-ligand system > with a total of 60686 atoms including water,ions and proteins, > it

[gmx-users] Error bar of order parameter

Dear Justin, in order to calculate the error bar for order parameter, i can't understand, which command exactly must be used? g_covar?g_anaeig? is it output of these commands? Many thanks -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Constraints errors

On 1/20/16 11:16 PM, Alireza Moradzadeh wrote: Dear Users, I want to simulate [BMIM][PF6] using following itp [ moleculetype ] PF6 2 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 P 1 PF6 P1 1 1.13 30.974 2 FP 1 PF6 F2 2 -0.33 18.998 3 FP 1 PF6 F3 3 -0.33 18.998 4 FP 1 PF6 F4 4

Re: [gmx-users] Error bar of order parameter

Please keep the discussion on the mailing list. On 1/21/16 8:23 AM, m g wrote: Dear Justin, I want to calculate the error bar for deuterium order parameter data for acyl chains of DPPC, for each carbons. I can calculate the Scd, i was learned it from your tutorial. but i don't know how can

[gmx-users] Not enough memory. Failed to calloc :

Dear all, i was trying run g_mmpbsa for trajectory of 100ns protein-ligand system with a total of 60686 atoms including water,ions and proteins, it ended up with the following error Fatal error: Not enough memory. Failed to calloc -1082130432 elements of size 4 for grps[j].nm_ind (called from

Re: [gmx-users] Error bar of order parameter

On 1/21/16 8:03 AM, m g wrote: Dear Justin, in order to calculate the error bar for order parameter, i can't understand, which command exactly must be used? g_covar?g_anaeig? is it output of these commands? "Order parameter" is ambiguous. What are you actually trying to do? After

Re: [gmx-users] Not enough memory. Failed to calloc :

On 1/21/16 5:50 AM, Nikhil Maroli wrote: Dear all, i was trying run g_mmpbsa for trajectory of 100ns protein-ligand system with a total of 60686 atoms including water,ions and proteins, it ended up with the following error Fatal error: Not enough memory. Failed to calloc -1082130432 elements

Re: [gmx-users] Not enough memory. Failed to calloc :

Thanks to Mark and Justin, my protein contains around 8000 atoms and ligand is around 33 atoms,and i used united atom ff, my workstation is with 64GB ram,but when i run the g_mmpbsa,i observed in performance monitor that there is no rise in memory usage,if it is shortage of memory is there any

[gmx-users] trivial question about water molecules

Hello Gromacs Users; I'd like to calculate the # of replaced water molecules by sodium chloride in my system . I added a 0.15M concentration of NaCl. How can I calculate the number of water molecules, which are replaced by ions? Thank you in advance, Marta -- Gromacs Users mailing list *

Re: [gmx-users] Not enough memory. Failed to calloc :

Hi, The memory use won't rise if there's a single large allocation that fails. The large negative number present in the error message indicates that the amount of memory asked for exceeded 2^31 bytes (because the quantity was larger than a signed 4-byte integer), which is unreasonable. You have

Re: [gmx-users] trivial question about water molecules

Check the original topology file without ions for the line SOL(number of water's here) then check the new topology file with ions-added for the same line and compare. === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge

Re: [gmx-users] trivial question about water molecules

On 1/21/16 11:47 AM, Marta Wisniewska wrote: Hello Gromacs Users; I'd like to calculate the # of replaced water molecules by sodium chloride in my system . I added a 0.15M concentration of NaCl. How can I calculate the number of water molecules, which are replaced by ions? genion replaces

Re: [gmx-users] GROMACS performance with an NVidia Tesla k40c

Hi, On Wed, Jan 20, 2016 at 6:35 PM, Michail Palaiokostas Avramidis wrote: > Hi, > > thanks for your answer. :) I tried to attach in the previous email > the log file but for some reason it never arrived on the list. Actually I > searched a bit more and the speed up

[gmx-users] Contact_Angles_Calculation

Dear GMX users, Recently, I want to analyze the contact angle of a gas bubble adsorbed on a surface, during the simulation, the bubbule can move freely on the surface. I aim to calculate the contact angle for each frame. Did anyone do such analysis and suggest a simple way to do it? I read

Re: [gmx-users] Contact_Angles_Calculation

See: http://pubs.acs.org/doi/abs/10.1021/acs.langmuir.5b00842 For a study using GROMACS. They code can be downloaded (though it might not be trivial to use). On Thu, Jan 21, 2016 at 6:32 PM, HZJ <1047334...@qq.com> wrote: > Dear GMX users, > > > Recently, I want to analyze the contact angle of

[gmx-users] Umbrella Sampling, Analysis Step

Dear Gromacs users, I've run the umbrella sampling. I could draw histograms with sufficient overlap, so I determined all of the simulations reached enough length of time. Now it's the analysis step. When I chose tpr files and pullf.xvg (forces) files as the input to wham, I was able to

Re: [gmx-users] Contact_Angles_Calculation

Thanks. I have come across this paper. It introduce how to calculate this angle. No code is provided with this paper. Can they share this code? I use a smooth surface. Best wishes! -- Original -- From: "Michael Shirts";; Date: Fri, Jan

Re: [gmx-users] Contact_Angles_Calculation

I believe the last line of the paper is: "We have made the code used for this analysis available on the GitHub site: https://github.com/shirtsgroup/droplet-analysis.; On Thu, Jan 21, 2016 at 10:02 PM, HZJ <1047334...@qq.com> wrote: > Thanks. I have come across this paper. It introduce how to