[gmx-users] About cutoffs for OPLSAA

Dear all, I want to study a system consisting of water, methane and CO2. I will use TIP4P/Ice , OPLSAA and EPM2 models respectively for the components . My problem is, how do I make a choice of the cutoff lengths, for a system which uses different molecular models which were

Re: [gmx-users] Fwd: Concatenating two trajectories

Hi, First of all, are you sure that you extended 2.xtc from 40ns? Can you post your trjcat output, which shows the starting frame of each trajectory. It should be like as shown below Summary of files and start times used: FileStart time Time step

Re: [gmx-users] Position Restraints with NVT and NPT

Thank you Justin! I understand usually for regular equilibration, restraints should be enough. But I am still wondering to what extent position restraint can restrain my atoms. In fact, I ran a relatively longer NVT using position restraints and I saw that both the absolute coordinates of my

Re: [gmx-users] Fwd: Concatenating two trajectories

Hello Venkat, Ya, I am sure that I use 1st.cpt to run next 40 ns job Find below the output of trjcat Summary of files and start times used: FileStart time Time step - complex_prod1_old.xtc0.000

Re: [gmx-users] Fwd: Concatenating two trajectories

So, that is the problem. Your second trajectory also has the same start time. Some how you didn't extend your second run from where your 1st run has finished. Out of curiosity, why is your time step 50ps? Its too big for a simulation. Generally it should be 2fs. On Mon, Apr 21, 2014 at 12:30

Re: [gmx-users] System coordinates not getting freezed

You're just trying to measure a potential energy, so do it the right way and don't get involved wiht making mistakes trying to freeze atoms. See http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy Mark On Mon, Apr 21, 2014 at 7:38 AM, sukriti002 sukriti...@e.ntu.edu.sg wrote: Hi

Re: [gmx-users] Concatenating two trajectories

Dear Sunita Are you sure you have added two trajectory files, one from 0 to 40 and the other from 40 onward ! Because Here *Summary of files and start times used: FileStart time Time step-

Re: [gmx-users] Fwd: Concatenating two trajectories

If you want to share a file, please use a file sharing service and share the link. Mark On Mon, Apr 21, 2014 at 7:32 AM, sunita gupta sunita@gmail.com wrote: Hello Everyone, I have two trajectories of 40 ns each, the first one is from 0 to 40 ns and next one is extended to next 40 ns

Re: [gmx-users] Fwd: Concatenating two trajectories

Hi Tsjerk, Sorry for the confusion. I thought its time step which is actually output writing frequency. Thank you sir for the correction. On Mon, Apr 21, 2014 at 2:39 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Venkat, That time step is the time step in the output trajectory. Yours

[gmx-users] all-angles

Dear Gromacs users I would like to know whether you have ever run a simulation with constraints in all-angles, or if you know about somebody who did it. When I try to run a protein with this option, it crashes, and only artificial systems like linear chains or modified small molecules seem to

[gmx-users] g_potential help

Hi All, I have a membrane-protein-solvent system, and I want the potential across the membrane in the direction of the membrane normal. I have 2 questions in that regard. 1) We know that epsilon_r = 80 for the water, ~7 for the membrane-water interface and ~2 for the hydrophobic membrane core.

Re: [gmx-users] Cannot write trajectory frame; maybe you are out of disk space

If you can rule out file permissions issues (because you wrote files earlier), and actually running out of disk, usually that would suggest a flaky network file system. Mark On Mon, Apr 21, 2014 at 4:09 PM, Andrew Bostick andrew.bosti...@gmail.comwrote: Dear gromacs users I am doing md

[gmx-users] Brownian Dynamics

Dear all, I noticed that Gromacs has the option to do Brownian Dynamics, is there anyone who has done that or where can I find any tutorials that can teach me to do it? Thanks. Sincerely Yutian (Shirley) Yang Biomedical and Chemical Engineering 329 Link Hall Syracuse University Syracuse NY

[gmx-users] How to fix or constrain Center of Mass

Dear Gromacs Users, Is there a way to constrain or fix Center of Mass of lipid bilayer or proteins in a MD run? Thanks! Thomas -- 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

[gmx-users] Cannot write trajectory frame; maybe you are out of disk space

Dear Mark Thanks for your reply. I am beginner in linux and gromacs. How to rule out file permissions issues? Which command is true for doing this? Please guide me to solve this problem. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Cannot write trajectory frame; maybe you are out of disk space

Did earlier frames get written? Use ls -l, gmxcheck etc. Google about file permissions - unlike on (say) an old Windows machine, on a compute cluster you will not be able to write files anywhere but where you're allowed to. Guessing here, because you haven't supplied any context. Mark On Mon,

Re: [gmx-users] g_potential help

On 4/21/14, 9:58 AM, rajat desikan wrote: Hi All, I have a membrane-protein-solvent system, and I want the potential across the membrane in the direction of the membrane normal. I have 2 questions in that regard. 1) We know that epsilon_r = 80 for the water, ~7 for the membrane-water

Re: [gmx-users] How to fix or constrain Center of Mass

On 4/21/14, 12:23 PM, Tom wrote: Dear Gromacs Users, Is there a way to constrain or fix Center of Mass of lipid bilayer or proteins in a MD run? To fix the position of the COM, use nstcomm = 1 (but your performance may suffer badly), otherwise removal of COM drift periodically is handled

Re: [gmx-users] [gmx-developers] Regarding Amber topology and co-ordinate file

Please ask usage questions on the gmx-users mailing list. The development list is for coding and planning discussions; this post is not appropriate here. I am CC'ing this message over to gmx-users. Please post anything further there. On 4/21/14, 10:28 AM, MOHD HOMAIDUR RAHMAN wrote: Dear

Re: [gmx-users] g_potential help

Hi Justin, So different parts of my system in Z-direction should be scaled differently, right? On a coarse level, aqueous part with a scaling of 80, membrane with a scaling of 2? How do I correct for this? Can I take the quantitative output for potential difference across a membrane in water from

Re: [gmx-users] g_potential help

On 4/21/14, 5:11 PM, rajat desikan wrote: Hi Justin, So different parts of my system in Z-direction should be scaled differently, right? On a coarse level, aqueous part with a scaling of 80, membrane with a scaling of 2? How do I correct for this? Can I take the quantitative output for

Re: [gmx-users] calculation speed of GROMACS and cut off parameters

On 4/21/14, 5:48 PM, mirc...@sjtu.edu.cn wrote: Hi everyone, I am using GROMACS to simulate bilayers, and I am testing two sets of parameters at present. However, I found significant differences of simulation speed of these two parameters sets. The mainly differences between these

[gmx-users] Cannot write trajectory frame; maybe you are out of disk space

Dear Mark Thanks for your reply. I googled file permission in linux OS. After that I did following steps: I created a directory entitled input. I put pdb and mdp files in the input directory. I used following command to change permission: chmod -R 777 input Now I will md simulation steps

Re: [gmx-users] Fwd: Concatenating two trajectories

Hello Venkat, Yeah, I think by default it will give 0 ps as start time for both trajectories and it should be set by user using -settime flag Correct me if I am wrong. Regards -- View this message in context: