Re: [gmx-users] g_sham

My bad, I had a typo, try this one: awk -v x=firstcoordmin -v y=secondcoordmin 'BEGIN{while(getline first_coordinate_file_here.xvg){if($0!~/#/$0!~/@/$0!~//){a[$1]=$2}}}NR0{if($0!~/#/$0!~/@/$0!~//){if(a[$1]==x$2==y){print $1}}}' second_coordinate_file_here.xvg === Micholas Dean

Re: [gmx-users] Membrane protein insertion

Hi, I used this method recently and I was experiencing the same errors. As Mark suggested, makes sure your protein survives an energy minimisation. My error was a result of poor preparation of the .pdb file before running pdb2gmx. My .itp file contained a long bond between the C and N termini of

[gmx-users] Coulomb barriers and Coulomb Softcore Potential

Dear Gromacs-Users, I want to calculate the solvation free energy of water in an aqueous ionic solution and I'm using the Python tool alchemical-analysis.py by Klimovich, Shirts and Mobley for evaluation. This tool demonstrates a very high N/N_k ratio (up to 7000) while decreasing the

Re: [gmx-users] Coulomb barriers and Coulomb Softcore Potential

Adjusting the soft core is a gigantic pain. I wouldn't recommend it, and it's likely not necesssary. What settings are you using now? Note that the manual describes how it is defined. Can you post the alchemical-analysis output for N/N_k? There's an analysis quirk we are looking at where the

Re: [gmx-users] Is dVremain/dl related to fep-lambdas?

That could be documented better. It is all of the changes in the molecule that are not explicitly occurring in their own lambda variable. For example, in setup 2, then all the changes have separate dhdl terms, so there is nothing left to be in dVremain/dl. Note that in setup 1) dVremain/dl is

[gmx-users] Heat autocorrelation function

Dear sir, How can i calculate the heat autocorrelation function in gromacs ? I want to calculate the thermal conductivity of noble gases. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post?

Re: [gmx-users] Heat autocorrelation function

On 24/08/15 09:25, Sunil Ghimire wrote: Dear sir, How can i calculate the heat autocorrelation function in gromacs ? I want to calculate the thermal conductivity of noble gases. I guess you need to run NVE simulations and store the energies often, then compute the autocorrelation function

[gmx-users] Membrane protein insertion

Hi all, I want to insert a membrane protein into a model bilayer and I've tried several methods. The more straightforward seems to be Memembed, which gives an orientation to the membrane. On the other hand this method only outputs the membrane as dummy balls. How to translate this orientation

Re: [gmx-users] Membrane protein insertion

Hi, Something isn't stable. Check that your membrane protein survives a vacuum EM (at least). And check your parameter settings for inflategro. Mark On Mon, Aug 24, 2015 at 9:53 AM Yasser Almeida Hernández yasser.almeida.hernan...@chemie.uni-hamburg.de wrote: Hi all, I want to insert a

Re: [gmx-users] Script to submit the md simulations on cluster.

Hi, No, we can't. Every cluster is set up differently. You have to consult your local documentation and sysadmins. That said, shell scripts tend to prefer NAME=value ie without spaces Mark On Mon, Aug 24, 2015 at 7:28 AM Seera Suryanarayana paluso...@gmail.com wrote: Dear gromacs users, I

[gmx-users] Is dVremain/dl related to fep-lambdas?

Dear gmx-users, When I compute with gromacs-5.1 relative free energies using mixed topologies (i.e. by setting typeA, typeB, bond kA, kB ant etc) I see that some undocumented value dVremain/dl is printed in log- and xvg-files. Please, clarify the exact meaning of the dVremain/dl quantity. How

Re: [gmx-users] mdrun writes gro file in two different formats and failed visualization of trajectories

Dear Justin Thanks for the reply. If that's the case what position of atoms the coordinates in trr file represents?. If I got you right, the coordinates in trr file neither get along with the mdrun generated gro file due to domain decomposition (hence broken molecules) nor with the trjconv

[gmx-users] Lambada + InflateGRO2 and membrane protein simulation

Dear All, Is any on-line server related to Lambada + InflateGRO2, which can gives the PDB file of the target membrane protein for simulation, including the coordinates of the surrounding lipid bilaylayer molecules? I am looking forward to getting a reply from you. Best regards. Brett

Re: [gmx-users] pairwise h-bonds

Sorry I had a typo in my previous email: I have used the -hbm and -hbn option (not the -m as it does not exist). The problem is however that this option gives me the h-bonds for each residues of group 1 to _any_ residue of group 2 and not the pairwise h-bonds between all members of group 1 and

Re: [gmx-users] simulations of ice beginning to spin

The box is defined by numbers at the last line of the GRO file. The point is that we do not know what happens with the box definition during the simulation. From what I could see at the final snapshot, the box in gromacs became cubic (based on location of molecules). On Mon, Aug 24, 2015

Re: [gmx-users] simulations of ice beginning to spin

On 8/24/15 4:02 PM, Nathan K Houtz wrote: Thanks for your reply. How do I get gromacs to recognize that I want a triclinic box? I thought it was simply defined in the .gro file (as VMD recognizes). I know I can use gmx editconf to modify the gro file to define a triclinic box, but do I need

Re: [gmx-users] calculate avarage and maximum non-bonded energy between energy groups

1) g_energy 2) g_analyze -f energy.xvg 3) Divide by 3 I do not know the physical sense of the maximum interaction energy. On Mon, Aug 24, 2015 at 4:25 PM, Tushar Ranjan Moharana tusharranjanmohar...@gmail.com wrote: Hi everyone, I want to calculate the average and if possible maximum

Re: [gmx-users] mdrun writes gro file in two different formats and failed visualization of trajectories

On 8/24/15 5:39 AM, anu chandra wrote: Dear Justin Thanks for the reply. If that's the case what position of atoms the coordinates in trr file represents?. If I got you right, the coordinates in trr file neither get along with the mdrun generated gro file due to domain decomposition (hence

Re: [gmx-users] simulations of ice beginning to spin

Thanks for your reply. How do I get gromacs to recognize that I want a triclinic box? I thought it was simply defined in the .gro file (as VMD recognizes). I know I can use gmx editconf to modify the gro file to define a triclinic box, but do I need anything in my input file? Thanks, Nathan

[gmx-users] calculate avarage and maximum non-bonded energy between energy groups

Hi everyone, I want to calculate the average and if possible maximum non-bonded energy between different energy groups. I used gmx energy whose out put was energy vs time. I want different energy groups in X axix and energy (average and/or maximum) in Y axis. A matrix of N X N describing energy

[gmx-users] Randomly alter pdb start coordinates

There is mentioned that for re-running an MD run for better statistics, it can be good to change starting coordinates, besides the seed, is there a gmx command which is used for randomly change starting coordinates of a pdb file? I need such a command or script for a PBS script which

Re: [gmx-users] Heat autocorrelation function

I want to use green- kubo formalism , which uses the integral of autocorelation of heat flux J to calculate thermal conductivity. On 24 Aug 2015 13:25, David van der Spoel sp...@xray.bmc.uu.se wrote: On 24/08/15 09:25, Sunil Ghimire wrote: Dear sir, How can i calculate the heat

[gmx-users] Single point energy calculations

Hello all, I am trying to calculate the single point energies of my system (a nucleic acid and a nanoparticle) to ultimately estimate the E(interaction). I am following this paper.