Re: [gmx-users] GROMACS 4.6.4 is released

Will a simulation from 4.6.1 continue running fine if I upgrade to 4.6.4? > Hi GROMACS users, > > GROMACS 4.6.4 is officially released. It contains numerous bug fixes, and > some noteworthy simulation performance enhancements (particularly with > GPUs!). We encourage all users to upgrade their ins

Re: [gmx-users] Energy minimization has stopped....

What does your curve look like? What parameters are you using in the mdp? How big is your system and what kind of molecules are in there? Providing this kind of information would help people work out what the problem is. Then again it may be ok that the minimisation has converged without reaching

Re: [gmx-users] Lysozyme in Water at different pH and Ionic strength

I notice that both papers mention modifications to GROMACS and cite the following: http://www.ncbi.nlm.nih.gov/pubmed/16471903 > Following up on Justin's reply I just want to add that, not only is it > possible, as it has been done before. For instance: > > http://www.ncbi.nlm.nih.gov/pubmed/18214

Re: [gmx-users] Re: gmx-users Digest, Vol 114, Issue 91

I think ProDy can do this. It is a python module for analysis of structures that can be downloaded from http://www.csb.pitt.edu/ProDy/ I'm not sure it can read xtc but you can probably use it after converting trajectories to pdb. >> On 10/30/13 11:26 AM, Knapp Bernhard wrote: >>> Hi users, >>> >>>

Re: [gmx-users] Lysozime in Water

Yes, I would use the same command to continue the simulation after stopping with the addition of -cpi Every time a .cpt is made, the previous one is renamed _prev.cpt so that you can still get it in case something happened in between the two. Normally I would use the .cpt but if that doesn't work

Re: [gmx-users] mdrun cpt

You're welcome On 28 Oct 2013, at 20:03, Pavan Ghatty wrote: > Aah yes of course. Thanks James. > > > > On Mon, Oct 28, 2013 at 3:16 PM, wrote: > >> No this isn't a problem. You can use job names under the -hold_jid flag. >> As long as you change the job name in the submit script between >>

Re: [gmx-users] mdrun cpt

No this isn't a problem. You can use job names under the -hold_jid flag. As long as you change the job name in the submit script between submissions this isn't a problem. You could have a submit script for job 4 with -N md_job4 and -hold_jid md_job3 then change these to -N md_job5 and -hold_jid md_

Re: [gmx-users] nstcalclr bug?

I think nstcalclr would only do something if you have longer range interactions to calculate (lr means longer than rlist). Therefore something has be longer than rlist for this to happen. > Hi there, > > I am using gromacs-4.6.1 with this mdp file: > > integrator= md; leap-frog int

Re: [gmx-users] pbc problem

I usually use -pbc nojump for my protein simulations and this works every time. > Dear gromacs users > > My system contains DOPC + CHOLESTEROLO + WATER + drug molecules in a > rectangular box. > > I put drug molecule in 2 position: a) drug in the center of bilayer > membrane, b) drug inside water

Re: [gmx-users] a new GROMACS simulation tool

Please could I have an account too. > Hi Everyone, > > I'm writing to let you guys know that we have developed a web-based tool > MD > simulation tool for GROMACS. It is a software package primarily developed > for biological MD and offers a huge amount of possible options and > settings > for ta

Re: [gmx-users] Molecular dynamics with LEGO?

Hi Tsjerk, In my opinion, we don't need to develop LEGO specifically for this - something already exists, which I played with in school. The molymod pieces (http://www.molymod.com/) already include bendy pieces, which are the next step on the lego website you advertise. Best wishes James > Hi :)

Re: [gmx-users] Re: Hai friends (balu)

I suppose there would also be a way of passing do_dssp output on to make_ndx then you could use the index with g_hbond to count hbonds in each secondary structure element. Best wishes James > If the goal is to simply count the secondary structure, pass the dssp > output file through grep "__" dss