[gmx-users] Error of mdrun

Dear Experts, Hi ! I am doing MD simulation on two computer, on one when I want to start the EM and do the mdrun command the following error results: linux:~/project # mdrun -v -s em.tpr -c em.pdb mdadm: /dev/md-v not identified in config file. linux:~/project # mdrun -v -deffnm em mdadm: option

[gmx-users] confirm bdd22a55a5075c60cd9dc4382a75e0b7689a1d11

Sir/Mam, please tell me what program in Gromacs have I to use to know how many water molecules reacting on the surface of the solute molecule in the cubic box about 3.0A unit distance from the surface of the solute. kind regards Munusamy e.mail:[EMAIL PROTECTED]

Re: [gmx-users] water can't freeze

Wei, Xiupeng wrote: Hi gmx users, I'm a new Gromacs user. Till now, I can get pretty good simulation of ice melting to water, but why can't I simulate water freezing to ice? The .top and .gro files used for water freezing simulation are generated by ice melting to 310K. I chan

[gmx-users] water can't freeze

Hi gmx users, I'm a new Gromacs user. Till now, I can get pretty good simulation of ice melting to water, but why can't I simulate water freezing to ice? The .top and .gro files used for water freezing simulation are generated by ice melting to 310K. I changed the temperature in

[gmx-users] Water in graphite plates

Dear All, I want to model water transport sandwitched within two graphite surfaces. Do you know how to generate the structure file of graphite surface? Thank you very much! Hero Be a better friend, new

Re: [gmx-users] residual negative charge?

Hi Victor, Assigning the right parameters for a molecule is a difficult task, and a single run of PRODRG is usually just the beginning. Search the archives and maybe also the wiki for more information, and read a few papers where simulations of proteins were done with hetero-molecule if you haven'

[gmx-users] residual negative charge?

Hello everybody, I'm trying to use gromacs to model an aza-type macrocycle (17 atoms around the ring). The structure does not include any aminoacids or sugars so, I'm building the itp file by hand. I started with a base topology from the PRODRG server and then added all the missing hydrogens

Re: [gmx-users] Conformation search!

On Friday 18 April 2008 10:37 am, Mark Abraham wrote: > Anthony Cruz wrote: > > > You seem to want to let your domains move relative to each other, but > > > > > > also to deny them much internal freedom. So what you want to do is > > > > > > enforce (some of) their internal structure. Thus, u

Re: [gmx-users] trjconv error

Ragothaman Yennamalli wrote: I wanted to truncate a trajectory file and when I use trjconv tool, I get an error: Fatal error: /media/usbdisk1/paul_case4/full_10ns_040408/traj2.xtc is not a trj file, exiting The file is able to read by gmxcheck... What could be the problem? What GROMACS versio

Re: [gmx-users] Conformation search!

Anthony Cruz wrote: > You seem to want to let your domains move relative to each other, but > also to deny them much internal freedom. So what you want to do is > enforce (some of) their internal structure. Thus, use distance restraints. > > Mark Thank you for your answer. But probab

Re: [gmx-users] Conformation search!

Dear Anthony, You can apply distance restraints to pairs of atoms, e.g. CA atoms in your domains. Check the manual. Ran. Anthony Cruz wrote: > > On Thursday 17 April 2008 9:13 pm, Mark Abraham wrote: > > > Anthony Cruz wrote: > > > > Hi User: > > > > We have a protein with two domains. This two

Re: [gmx-users] Concatenate TPR files after restart

There is no need to concatenate .tpr files; they contain structure and parameter information, and thus is does not make sense to add them together. To analyze the whole trajectory, supply g_hbond the starting .tpr file along with your trajectory file. -Justin -- Ok Jus

Re: [gmx-users] Conformation search!

On Thursday 17 April 2008 9:13 pm, Mark Abraham wrote: > Anthony Cruz wrote: > > Hi User: > > We have a protein with two domains. This two domains were connected by > > two linkers of different length. We want to study the different > > conformation that the protein domains can adopt depending the

[gmx-users] trjconv error

I wanted to truncate a trajectory file and when I use trjconv tool, I get an error: Fatal error: /media/usbdisk1/paul_case4/full_10ns_040408/traj2.xtc is not a trj file, exiting The file is able to read by gmxcheck... What could be the problem? Thanks in advance. Regards, Ragothaman Ex