[gmx-users] Showing different RMSD values

Dear gromacs users I have done simulations for 100ns two times with similar conditions of 20 residue length peptide. I have plotted the RMSD graph. The average RMSD values for simulations are 0.486 and 0.4102. My question is why I didn't get similar average RMSD values even though the conditions f

[gmx-users] Fwd: Difference in Hydrogen Bond Lifetimes on using pbc

Dear All, I've carried out a 100ns simulation of protein in water and want to calculate hydrogen bond (forward) lifetime between Protein-Water. I tried g_trjconv with application of -pbc mol -ur compact options on untruncated(100ns) trajectory. The results came as: *ACF 11303/11303No

Re: [gmx-users] Surface tension for water

Dear Dan, As you can see in the images I sent to you, there is no error massage in output files. The properties of the system such as pressure or temperature is so high, that's why I've concluded that the system is crashed. Sincerely, Iman On Wed, Aug 30, 2017 at 12:44 AM, Iman Ahmadabadi < iman

Re: [gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa

Hi, I will download and install APBS and try again. I have already tried pre-compiled version of g_mmpbsa from the link you suggested. Thanks Best Regards, *Neha* Research Scholar, Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pra

Re: [gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa

Hell, Download APBS and install it then use the binary package of g_mmpbsa. or see here: Pre-compiled executable program Pre-compiled program does not require any external library or GROMACS and APBS package. These programs are standalone and without any dependency. Download, extract and use it.

Re: [gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa

Hello, I have not installed APBS. I have compiled g_mmpbsa without APBS. Should I compile it with APBS? Best Regards, *Neha* Research Scholar, Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, On Wed, Aug 30, 2017 at 10:23

Re: [gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa

Hi, The segmentation fault error during polar energy calculations is due to APBS. I don't know whether you installed it properly or not. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read h

[gmx-users] Pure repulsive LJ potential for OPLSAA

Hi, gmx users, I am wondering how can I set up a pure repulsive or attractive LJ potential in the OPLSAA force field. Since you need to set up the sigma and epsilon instead of C6 or C12, the pure repulsive requires sigma to be infinity and epsilon need to be 0. Is there a way to achieve pure repuls

Re: [gmx-users] Surface tension for water

Iman, You get the error message in the terminal if you are running it on your own machine. If you are running on a supercomputer, the error messages will be directed to a file. How do you know the simulation is crashing without the software telling you? Please find the message (check all outputs),

Re: [gmx-users] Surface tension for water

Hi Dan, There is no error massage, It's just a crashing and stopping the simulation. The version is 4.6.0. Iman On Tue, Aug 29, 2017 at 9:57 PM, Iman Ahmadabadi wrote: > Dear Dan, > > I have attached the NPT.mdp file in the following: > > title = NPT equilibration > ; Run parameters > integra

Re: [gmx-users] Surface Tension Calculation

Hi, Dan, Thanks for your response. The interfacial tensions I get from gmx energy is way larger than the typical surface free energy of solid. So I suspect the freeze command may have generated some artifacts and I need to find a better force field. -- Gromacs Users mailing list * Please search

Re: [gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa

Thank you for replying, I have compiled g_mmpbsa without apna. I have tried with pre-compiled binary as well but no success. On 29-Aug-2017 3:45 PM, "Nikhil Maroli" wrote: > [image: Boxbe] This message is eligible > for Automatic Cleanup! (scinik...@gmail.com)

Re: [gmx-users] Surface tension for water

Hi Iman, What version of Gromacs are you using? What is the error message? Dan On Tue, Aug 29, 2017 at 1:27 PM, Iman Ahmadabadi wrote: > Dear Dan, > > I have attached the NPT.mdp file in the following: > > title = NPT equilibration > ; Run parameters > integrator = md > nsteps = 2000 > dt

Re: [gmx-users] Surface tension for water

What is the error message? On Tue, Aug 29, 2017 at 1:27 PM, Iman Ahmadabadi wrote: > Dear Dan, > > I have attached the NPT.mdp file in the following: > > title = NPT equilibration > ; Run parameters > integrator = md > nsteps = 2000 > dt= 0.001 > > ; Output control > nstxout = 500 > nst

Re: [gmx-users] Surface tension for water

Dear Dan, I have attached the NPT.mdp file in the following: title = NPT equilibration ; Run parameters integrator = md nsteps = 2000 dt= 0.001 ; Output control nstxout = 500 nstvout = 500 nstenergy = 500 nstlog = 500 ; Bond parameters continuation= no constraint_algorithm=

Re: [gmx-users] pullx (gromacs 4.6 vs 2016)

Hi All, Am just wondering if somebody has seen this in different gmx versions? Thanks. JIom On Fri, Aug 25, 2017 at 11:00 AM, gromacs query wrote: > Hi All, > > I am using 'equivalent' mdp settings for pull run in Gromacs 4.6 and 2016. > > With gromacs 4.6 I get time, 0Z and 1dZ; which I can

Re: [gmx-users] Surface Tension Calculation

Hi Lei, 1. In the Gromacs manual you can find the formula that the software uses to calculate surface tension. It is just based on a few components of the pressure tensor, so I imagine you can just use gmx energy (or g_energy depending on the version of Gromacs you are using). 2. Freezing doesn't

Re: [gmx-users] Surface tension for water

What is the error message? What version of Gromacs are you using? Can you post the entire .mdp file? On Tue, Aug 29, 2017 at 9:34 AM, Iman Ahmadabadi wrote: > Dear All Users, > > I'm calculating the surface tension of the water, my box contains almost > 5000 water molecule in the middle of that

[gmx-users] Surface tension for water

Dear All Users, I'm calculating the surface tension of the water, my box contains almost 5000 water molecule in the middle of that. Through NVT equilibration, I got reasonable results for surface tension but when I use NPT for my system, the system crashes every time. The pressure coupling options

Re: [gmx-users] Difference in hydrogen bond lifetimes with and without pbc

Dear Eric and other Gromacs users, Thanks for clarifying about how different timescale of trajectories can affect lifetimes But the case with and without pbc have same length of trajectories (100 ns). Then why the difference in lifetimes ( 1793ps with pbc and 2345 without pbc) Which can be regarded

Re: [gmx-users] gmx analyze Luzar analysis

Thank you! But still I do not understand what those values represents since there isn´t a legend in the gmx analyze output. I understood that those 3 values should be the average hbond lifetime, and the 2 constant k and k´. Am I correct ? The fitting is bad since I used long simulation time analy

Re: [gmx-users] Difference in Hydrogen Bond Lifetimes on truncating trajectory and also on using pbc

Dear Apramita, Right. Still, the same still applies with regards to the -666. It could be a matter of statistics, why you get sensible values for the longer trajectory chunk. Also, note that the trajectory length limits the possible timescales that the model can tease out. If I understand corre

Re: [gmx-users] Difference in Hydrogen Bond Lifetimes on truncating trajectory and also on using pbc

Dear Eric, Its actually the DG(kj/mol) value which is -666. The time is coming to be-126 ps. But the g_hbond is failing to fit the kinetic model to the data for the last 60ns as you have implied. Any reasons why this could have happened, while for the entire trajectory, I am getting positive value

Re: [gmx-users] gmx analyze Luzar analysis

Dear Valerio, Have a glance at the paper by Luzar and Chandler. Btw: your data doesn’t fit with the kinetic model very well, hence the -666 for the integral. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Ch

[gmx-users] gmx analyze Luzar analysis

Dear all, I am trying to obtain parameters for h-bonds. I used the tool gmx hbonds with -ac option but resulted in segmentation fault. Therefore from the normal gmx hbond output I used gmx analyze to obtain the autocorrelation function. Therefore, using again gmx analyze with -luzar options and th

Re: [gmx-users] Unable to install 5.1.14

Installing version 2016.3 worked perfectly. Thanks! Regards, Rajat On Mon, Aug 28, 2017 at 12:08 PM, Vytautas Rakeviius wrote: > You have updated boost so you have to update GROMACS too. 2016.3 is the > latest version you should download it. > Another possibility is to downgrade boost to older,

Re: [gmx-users] gromacs error

On 8/29/17 12:09 AM, Neha Gupta wrote: Hi Vytautas, Thank you for your response.. I did as you told and got this message at the command prompt libfftw3f: /usr/local/lib/libfftw3f.la /usr/local/lib/libfftw3f.a But the error tells me : gmx: error while loading shared libraries: libfftw3f.so.

Re: [gmx-users] nstcomm < nstcalenergy

On 8/29/17 1:47 AM, Simon Kit Sang Chu wrote: Dear every user, I am using Andersen thermostat and nstcomm should be set to 1 (step). However, after specifying nstcomm = 1, an error has returned - nstcalenergy cannot be smaller than nstcomm. GROMACS automatically sets it to nstcalenergy step.

Re: [gmx-users] nstcomm < nstcalenergy

Hi， Firstly, you should confirm your gromacs version, gromacs 5.x certainly includes nstcalenergy options in .mdp file. So you must set nstcalenergy=1 while the default value is 10 in .mdp if you want to nstcomm=1. thanks -- Gromacs Users mailing list * Please search the archive at http://w

Re: [gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa

Hi, Install Pre-compiled executable program You might wrongly be compiled for : Includes APBS functionality use with To use with external APBS program -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can

[gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa

Dear Sir/Ma'am, I am trying to run g_mmpbsa for gromacs-5.1.2. It is working fine for MM energy and apolar energy but when I am trying to run this for polar energy, g_mmpbsa run is stopping giving error: Segmentation fault (core dumped). Previously I was using gromacs 4.6 with same g_mmpbsa versi

Re: [gmx-users] Difference in Hydrogen Bond Lifetimes on truncating trajectory and also on using pbc

Dear Apramita, IIRC, the time is set to.-666 when gmx hbond fails to fit the kinetic model to the data. Not the most informative way of indicating an error perhaps. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department