[gmx-users] REMD exchange probabilities

Dear list, Using an exchange probability of 0.25 and temperature range 293-370 K, I calculated number of replicas using the server. However, when I did first run and tried exchanging replicas every 500 steps (1 ps), I don't think the exchange probabilities make sense in particular replicas 15

[gmx-users] definition of eigenvector in gromacs

Dear All, Recently I have read a gromacs related article which contain a sentence Trajectories pojected on the first two eigenvectors. Will you please tell me the meaning of eigenvector and Trajectories pojected on the first two eigenvectors? Will you please also explain it to me using

[gmx-users] Separate .xtc file according to the result from g_cluster

Hi, Is there any short way to seperate the .xtc file according to the results from g_cluster? For example, I want to chop the .xtc file into several small trajectories, each includes all the snapshots from the clusters given by g_cluster? Thank you, -- Gromacs Users mailing list * Please

Re: [gmx-users] topology include file gmx43a1.ff/ffG43a1.itp not found

On 3/7/15 11:03 PM, marzieh dehghan wrote: Hi every body I want to perform molecular dynamics using gromacs for a covalent bond, so I used topol build to create a topology file. after holding the following command: grompp -f ions.mdp -c test.gro -p test.top -o ions.tpr I confronted this

Re: [gmx-users] topology include file gmx43a1.ff/ffG43a1.itp not found

Hi, None of these are names of files present in share/top of your GROMACS installation directory. Look there, and choose accordingly. Mark On 08/03/2015 5:04 am, marzieh dehghan dehghanmarz...@gmail.com wrote: Hi every body I want to perform molecular dynamics using gromacs for a covalent

Re: [gmx-users] Embedding protein into lipid bilayer

Justin Lemkul jalemkul@... writes: On 3/6/15 11:02 PM, yoochan wrote: Dear GMX users, I’m tyring to build lipid and transmembrane(protein) system using inflategro.pl. in GROMACS 5.0.4. I think the inflategro.pl can not build a result on center of box when the membrane or

Re: [gmx-users] GMX5.0 g_select

On 07/03/2015 9:19 pm, xy21hb xy2...@163.com wrote: Dear Gmxers, What I meant is to use the result of g_select as index to calculate e.g. g_hbond, See gmx select -h about -on. gmx hbond has not been updated to use the selection code itself, but you can script the call to gmx hbond to

Re: [gmx-users] Separate .xtc file according to the result from g_cluster

Hi, gmx cluster -h is a good friend ;-) see the -cl option. Mark On Mon, Mar 9, 2015 at 1:49 AM, Xingcheng Lin linxingcheng50...@gmail.com wrote: Hi, Is there any short way to seperate the .xtc file according to the results from g_cluster? For example, I want to chop the .xtc file into

[gmx-users] Gromacs with InflateGro

Hi all, I'm really struggling to get InflateGro to work in a dimer + lipid (no water or ions) system. The fault seems to happen when the regular expression to break the .gro entry reads in an entry from C to C1. I managed to generalise the regex further and now using substr to