Re: [gmx-users] bilayer simulation crashes after 2 ns or 7 ns of stable runs. why does system explode

Hi, Sorry for the incomplete details. Here they are now: I started with a well-equilibrated POPC bilayer, and changed one POPC lipid to a lipid of my interest. I wrote the topology file for the new lipid accordingly. After that, I did some simple steepest descent minimization, and followed it up

Re: [gmx-users] bilayer simulation crashes after 2 ns or 7 ns of stable runs. why does system explode

maria goranovic wrote: Hi, Sorry for the incomplete details. Here they are now: I started with a well-equilibrated POPC bilayer, and changed one POPC lipid to a lipid of my interest. I wrote the topology file for the new lipid accordingly. This topology change is probably the source of the

Re: [gmx-users] (no subject)

Quoting Mahnam <[EMAIL PROTECTED]>: > In God We Trust > Hello GMX > users > I want to equilibrate my protein in a mix solvent, befor this > work, I made a cubic box that it contained 215 spc water and 5 proline > molecule (without protein) with 20*20*20 angestrom and then I minimized > it. wh

[gmx-users] (no subject)

In God We Trust Hello GMX users I want to equilibrate my protein in a mix solvent, befor this work, I made a cubic box that it contained 215 spc water and 5 proline molecule (without protein) with 20*20*20 angestrom and then I minimized it. when I do position restrain with NPT ensemble a

Re: [gmx-users] set up topology in free energy calculations

QL, 1. Yes. I'd use version a) because of, the less dummies, the better. 2. Yes 3. Of course, charges have to vanish for dummies, too. Keep the bonded terms. If not, your dummies will "diffuse" away. Yes, your assumption about dummies is right. Actually, I won't use this system for your first

[gmx-users] g_rmsf

Dear gmx users, I have a basic query. With respect to which structure are the rmsf values calculated per each atom? is it w.r.t average structure of the protein or the reference structure that we provide using -s option? I dont find any explanation of the output generated using g_rmsf. Please ma

Re: [gmx-users] g_rmsf

SWAPNA wrote: Dear gmx users, I have a basic query. With respect to which structure are the rmsf values calculated per each atom? is it w.r.t average structure of the protein or the reference structure that we provide using -s option? I dont find any explanation of the output generated usi

Re: [gmx-users] infinite molecule problem - Follow up info

Stop COM of the whole system? 2008/4/6 Bo Zhou <[EMAIL PROTECTED]>: > Dear gmx users, > > My previous question are: > > >I want to simulate the solid/liquid interface, so I build an infinite > inorganic molecule with pbc=full first. After I ran the system > > with vaccum (at the top of system)

[gmx-users] g msd freeze

Dear users, I would like to calculate the mean square displacement. Using the g_msd -f traj.xtc -s input.tpr -n index.ndx -o msd.xvg I get Reading file input.tpr, VERSION 3.3.2(single precision) Reading file input.tpr, VERSION 3.3.2(single precision) Group 0( C) has

[gmx-users] CPMD and gmx

Dear all, We successfully passed all test with CPMD-gmx and now the time to do md production runs, In examples from interface home page timestep is 1fs but in CPMD papers time step is much less, about 0.12 fs. Could you please advise some papers to read? I found only one paper referencing to CPMD-

Re: [gmx-users] CPMD and gmx

Dear Andrey, The maximum time step depends on whether you're doing Born-Oppenheimer or Car-Parrinello MD. In the case of usual BO MD, you normally want a time step of 0.5-1.0 fs, possibly 2 fs, if you use rigid molecules. In the CP case, you have to use a much smaller time step to make sure that t

Re: [gmx-users] Error gmxtest

Dear David, while ERROR for dec+water complex test is clear, I do not know what to make of this one: FAILED. Check files in acetonitrilRF from /gmxtest/complex/acetonitrilRF/md.log: Initializing LINear Constraint Solver number of constraints is 526 average number of constraints coupled to

[gmx-users] Re: infinite molecule problem - Follow up info

When I stopCM of the whole system, all running is ok, but I found the infinite surface oscillating along the xy plane collectively and frequently, so there were too much inconsistent shifts. Then I stopCM of the surface only, I get a lot of warnings about the Large VCM(group rest) (group rest = SOL

Re: [gmx-users] Error gmxtest

Have a look here: http://www.gromacs.org/pipermail/gmx-users/2007-November/030491.html Perhaps try downloading the new version and re-compiling. -Justin Quoting Nadia Gro <[EMAIL PROTECTED]>: > Dear David, > > while ERROR for dec+water complex test is clear, I do not know what to make > of t

[gmx-users] Langevin Dynamic "bd-temp" parameter

Hi, I tried to run a md calculation with a "bd-temp = 300" line in my file, but it gave a warning: "Unknown left-hand 'bd-temp' in a parameter file" Did I use the right parameter for setting up the temperature in Langevin Dynamics? Thanks for your help in advance. Simon Sham

[gmx-users] trjconv chaged the chain names of multi-chain complex?

Hi, Chain name is very important for some application. But, when I use the following script to get a minimized structure from a multi-chain complex. But the chain name was changed. I checked the man trjconv , but I did not find any information on chain name for trjconv. pdb2gmx -ff ${force

Re: [gmx-users] trjconv chaged the chain names of multi-chain complex?

Quoting Liu Shiyong <[EMAIL PROTECTED]>: > Hi, > > Chain name is very important for some application. But, when I use the > following script to get a minimized structure from a multi-chain complex. > But the chain name was changed. I checked the man trjconv , but I did not > find any informat

Re: [gmx-users] Langevin Dynamic "bd-temp" parameter

simon sham wrote: Hi, I tried to run a md calculation with a "bd-temp = 300" line in my file, but it gave a warning: "Unknown left-hand 'bd-temp' in a parameter file" Did I use the right parameter for setting up the temperature in Langevin Dynamics? No. Check out the extensive m

Re: [gmx-users] trjconv chaged the chain names of multi-chain complex?

Liu Shiyong wrote: Hi, Chain name is very important for some application. But, when I use the following script to get a minimized structure from a multi-chain complex. But the chain name was changed. I checked the man trjconv , but I did not find any information on chain name for trjconv

Re: [gmx-users] g msd freeze

Kateřina Hynštová wrote: Dear users, I would like to calculate the mean square displacement. Using the g_msd -f traj.xtc -s input.tpr -n index.ndx -o msd.xvg I get Reading file input.tpr, VERSION 3.3.2(single precision) Reading file input.tpr, VERSION 3.3.2(single precision