Re: [gmx-users] Autocorrelation times from gmx wham and analyze

Den 2018-09-05 kl. 13:01, skrev Gmx QA: Hi all, I am running a series of umbrella sampling simulations of a drug across a membrane, with the final aim to determine permeability using the local diffusion model. I have come across papers where the (necessary) autocorrelation times of the

Re: [gmx-users] i have a question about multiple chain simulation at the same box

On 9/5/18 9:25 AM, milad bagheri wrote: I'm going to examine the interaction between the two proteins using molecular dynamics simulation by gromacs, so I downloaded pdb code 5op1 from the rcsb , which has two protein(Complex). I want to create a gap between two protein, and then with the

Re: [gmx-users] Justin paper 2010 pulling

On 9/5/18 1:50 AM, Rakesh Mishra wrote: So that means It is may be due to the difference in the type of interaction. and I can not understand your this statement "you have to contend with forces principally acting perpendicular to the direction of the bias" Well, what interactions act

Re: [gmx-users] Orthorhombic structure and Lincs warnings

It's not the first time you're posting this message and there's a reason noone is replying. 1. What are the inter-axis angles of that orthorhombic box? Why not a rectangular box? 2. Why are you using LINCS with graphene, which should _not_ be simulated with constraints? 3. Why are you restraining

[gmx-users] Orthorhombic structure and Lincs warnings

Dear all, Can simulation for orthorhombic structure be done in gromacs? Actually I am working with 2-D graphene sheets which are like a parallelogram. In my system, there is a graphene sheet (restrained)and water. After the energy minimization, energy is coming positive (order of 10^8) On

[gmx-users] Pressure control with constraints incompatible with expanded ensemble

Hi all, I would like to use Gromacs (2018 versions on GPUs) to compute solvation free energies using expanded ensemble simulations. I have no problems in the NVT ensemble, but when I try and implement pressure control I run into errors. Specifically, if I want to use expanded ensemble, I must

[gmx-users] compilation terminated with error

Dear all, The compilation of the Gromacs.2018.2 on a cluster terminated with error in below step, would you please let me know how I can overcome the issue? I use gcc/7.3.0. [ 0%] Building C object src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/crc32.c.o cd

Re: [gmx-users] Workstation choice

Hi Olga, The authors of: https://github.com/bio-phys/MDBenchmark/tree/version-1.3.2 https://zenodo.org/record/1318123 May be helpful. If your data is not confidential, you may consider running Gromacs remotely on a cloud high performance computing resource, or benchmarking remotely and then

Re: [gmx-users] Calculating the Hydrophobic and Hydrophilic SASA values on GROMACS version 5.1.2

Hi Supid, Got the point. Thanks a lot. On Wed, Sep 5, 2018 at 2:05 AM, Sudip Das wrote: > Hi Andrew, > Follow the below link. Hope that helps. > > http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0 (follow > the 'g_sas' section) > > Regards, > Sudip > > On Wed, Sep 5, 2018 at

[gmx-users] i have a question about multiple chain simulation at the same box

I'm going to examine the interaction between the two proteins using molecular dynamics simulation by gromacs, so I downloaded pdb code 5op1 from the rcsb , which has two protein(Complex). I want to create a gap between two protein, and then with the same coordinate Put these two proteins in a box

[gmx-users] Autocorrelation times from gmx wham and analyze

Hi all, I am running a series of umbrella sampling simulations of a drug across a membrane, with the final aim to determine permeability using the local diffusion model. I have come across papers where the (necessary) autocorrelation times of the mean-squared fluctuation of the coordinates are

Re: [gmx-users] Calculating the Hydrophobic and Hydrophilic SASA values on GROMACS version 5.1.2

Hi Andrew, Follow the below link. Hope that helps. http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0 (follow the 'g_sas' section) Regards, Sudip On Wed, Sep 5, 2018 at 9:56 AM Andrew Srimalka Wijesekera < 2014s14...@stu.cmb.ac.lk> wrote: > Dear all, > > I'm currently studying

[gmx-users] Workstation choice

Hello, I need help in choice of the workstation for MD simulations using GROMACS. It is supposed to study systems consisting from 30-50k atoms, in particular, lipid bilayer models. Since the last generation of Intel and Ryzen CPU has made a big leap in performance, available workstation can’t be