Re: [gmx-users] difference in -heavyh and -deuterate

Hi, With heavyh you redistribute the mass of the system, making hydrogen heavy by taking mass from the attached atom. In that way the total mass remains unchanged, but you can use a bigger time step (I think it's meant for 4fs). Felipe On 21/07/15 07:28, Sana Saeed wrote: what is the main

Re: [gmx-users] g_msd and Diffusion Constant

Yeah. Generally, what my observation says that in xvg file you have the round up value which has 4 decimal digits. But for your one it has 10 decimal degits. Can you please try with a higher version- 4.6.x? On Tue, Jul 21, 2015 at 10:44 AM, Ganesh Shahane wrote: > Hi! > > I am using gromacs ve

[gmx-users] difference in -heavyh and -deuterate

what is the main difference between -heavyh and -deuterate. i know the only difference, that is in deuterate the mass is increased by 2 amu and in -heavyh by 4 factor. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List befor

[gmx-users] (no subject)

hican we use multiple files as input in pdb2gmx. i want to merge two different proteins into one coordinate file ad also its topology in one file, for that i am using -merge, but it gives error in reading second pdb file. -- Gromacs Users mailing list * Please search the archive at http://www.

Re: [gmx-users] g_msd and Diffusion Constant

Hi! I am using gromacs version 4.5.5. The values are different. The value displayed on the terminal screen is 0.0007417*1e-5 cm^2/s while the value displayed in the chol.xvg file is 0.000903331*1e-5 cm^2/s. As you can see, both values are quite close though the value in chol.xvg doesn't appear to

Re: [gmx-users] g_msd and Diffusion Constant

Hi!! Are the values different? Can you show us both the values? I presume both values would be same. The value in the xvg file would be round up. Chandan On Tue, Jul 21, 2015 at 1:33 AM, V.V.Chaban wrote: > which version fo you use? > > > > > > On Mon, Jul 20, 2015 at 8:28 AM, Ganesh Shahane

Re: [gmx-users] g_msd and Diffusion Constant

which version fo you use? On Mon, Jul 20, 2015 at 8:28 AM, Ganesh Shahane wrote: > Dear Gromacs Users, > > I have performed a simulation of a POPC+Cholesterol bilayer. I wish to know > the diffusion constant of a particular cholesterol molecule. Towards this, > I performed a g_msd using the c

[gmx-users] segmentation fault

Dear all, what is the solution for the segmentation fault after applying electric field? when I enter 1 for number of cosines mdrun doesnt start with segmentation fault error. does it mean that i can write any numbers as number of cosines and have stationary electric field or should i enter 1 only?

[gmx-users] End-to-End Vector Relaxation Time

Hi All, I have a 1 micro-second trajectory of a 11-residue peptide in explicit solvent. I want to calculate the end-to-end vector relaxation time for the peptide segment. Now, during post-processing the raw trajectory file, I ran the following commands 1. trjconv -s md.tpr -f md.trr -o md-p

[gmx-users] angle between two vectors

Dear Gromacs users, with which tool of gromacs can compute the angle between two vectors of different atoms number? Thanks! -- Natalia Alveal Fuentealba Ingeniera en Bioinformática Laboratory of Structural Biology and Nanophysiology Departament of Physiology Pontificia Universidad Católica de Chi

Re: [gmx-users] GMXPBSA

Hi, Please have look here: GMXPBSA 2.1: A GROMACS tool to perform MM/PBSA and computational alanine scanning http://www.sciencedirect.com/science/article/pii/S0010465514003154? Contact me in private if you need help Best And Il 20/lug/2015 16:19 Urszula Uciechowska ha scritto: Dear gromacs

Re: [gmx-users] Enforced rotation errors

Dear Anthony, the problem you are experiencing with the ‘flex’ rotation potential could be related to the rotation group moving too far along the direction of the rotation vector. As for V_flex, the slabs are fixed in space, the rotation group may after some time enter a region where no reference

Re: [gmx-users] md-vv and md

Please check my last e-mail I gave some more information about my system and energy results. Here is the link for plots http://imgur.com/HobCa8H,shH3pA9,OZpCUTZ,DeDk35Q,iFDGzXW,67SHwUw,Jj572Wx,2E1TJuH,xNC3D1s,JChHqjO,Z5Uu1l1,2mKA8UO,9DSe8OO#2 On Sat, Jul 18, 2015 at 4:13 AM, Michael Shirts wrote

[gmx-users] Umbrella sampling - abnormal potential energy profile and wrong PMF profile

Dear gromacs users, My simulation system has 512 water molecules covered by 25 organic molecules on each side (1st pic). I have also gas phase. Link for the plots : http://imgur.com/HobCa8H,shH3pA9,OZpCUTZ,DeDk35Q,iFDGzXW,67SHwUw,Jj572Wx,2E1TJuH,xNC3D1s,JChHqjO,Z5Uu1l1,2mKA8UO,9DSe8OO#0 In order

[gmx-users] Enforced rotation errors

Dear All, I hope you can help. I am using 'flex' enforced rotation to rotate a cylindrical protein along the surface of a globular protein. Unfortunately my system is experiencing what I can only assume is an IO problem: DD step 94 load imb.: force 2.9% pme mesh/force 0.677 S

[gmx-users] GMXPBSA

Dear gromacs users, I would like to run BFE calculations with gromacs. I performed MD simulations for 100ns and would like to extract snapshots from the MD and split them into the complex, protein and DNA. My question is how many sps should I extarct from the MD? and Are there any scripts availa

Re: [gmx-users] Histogram result in free energy calculation

Thank you for kind answer, After I ran the simulation, the all values resulted from Free energy calculation in Justin tutorial were almost same. But I have difficulty in drawing histogram using xmgrace. Whenever I draw the histogram, it showed totally different with the figure in tutorial.. Rec

[gmx-users] Gromacs 5.0.5 compilation error

Hi all, I am compiling Gromacs 5.0.5 and got this error: ../../lib/libgromacs_mpi.so.0.0.0: undefined reference to `__cudaInitModule' collect2: error: ld returned 1 exit status make[2]: *** [bin/template] Error 1 make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2 make: *** [all] E

Re: [gmx-users] segmentation fault

On 7/19/15 8:32 PM, Sikandar Mashayak wrote: Hi, I am trying to simulate a confined water system with gromacs 5.0.5, however, I am getting the segmentation fault. Below are the gdb backtrace and the build info. Without an .mdp file and description of what you've done so far, there's little

Re: [gmx-users] Questions about GROMACS capabilities

On 7/19/15 7:55 PM, Eric Smoll wrote: Hello GROMACS users, I have a few questions about what is possible in GROMACS: 1.) Is it possible "reset" the velocity of a subset of molecules in a MD simulation to an arbitrary, non-thermal distribution? I am particularly interested in the situation whe

Re: [gmx-users] g_hbond : normalization autocorrelation function.

On 7/19/15 10:55 AM, Nilesh Dhumal wrote: Erik, I want autocorrelation function without normalization. Use the -nonormalize option. -Justin Exact value at t=0, t=1 is with normalization. Nilesh Hi Nilesh, I’m not sure what you mean. Both Ac_finSys and Ac are 1 at t=0. What normali

Re: [gmx-users] MD exit condition

On 7/19/15 9:16 PM, Eric Smoll wrote: Hello Gromacs users, In response to a question on setting a group-group distance as an MD exit condition, Mark Abraham suggested that it might be possible to use a table-specified bond that would terminate a simulation by generating an infinite force and c

[gmx-users] g_msd and Diffusion Constant

Dear Gromacs Users, I have performed a simulation of a POPC+Cholesterol bilayer. I wish to know the diffusion constant of a particular cholesterol molecule. Towards this, I performed a g_msd using the command as follows- g_msd -f 30chol.xtc -s prod.tpr -lateral z -endfit 80 -n index.ndx -mol

[gmx-users] segmentation fault

Dear all, for applying electric field in gromacs-4.5.5 I should enter 3 numbers. The first one is number of cosines that should be 1. any number smaller than 1 is acceptable but when I use 1, grompp is done but mdrun doesnt start with the following error: segmentation fault. What should I do? Is it