Re: [gmx-users] average structure with ligand

Be sure to see http://wiki.gromacs.org/index.php/Average_Structure for help interpreting results. On Tue, Mar 18, 2008 at 2:16 AM, Ran Friedman <[EMAIL PROTECTED]> wrote: > Dear Anna, > > Use make_ndx to create any group you find useful. > > Ran. > > > > Anna Marabotti wrote: > > Dear gmx-user

Re: [gmx-users] Free energy of dihedral restraint

Bob, I don't believe that it is implemented. Developers: It probably should be, since the other restraints can be perturbed. In the interim, it's pretty straightforward to compute the dV/dlambda for restraining from the restraint energy if you know the value of the dihedral angle (which you can e

Re: [gmx-users] problem about rmsd

sudheer babu wrote: Thanks for your reply, I am mentioning commands, from crashing the simulation 1. tpbconv -f protein.trr -s protein.tpr -e protein.edr -n index.ndx -o out.tpr Look closely at the output here, and your original nstvout .mdp value. Unless you wrote velocities every picosec

Re: [gmx-users] problem with grompp (that is used instead of tpbconv)

OZGE ENGIN wrote: Hi David, I did what you suggested but encountered with a problem similar to one encountered by tpbconv command. I got the following error: Reading frame 4 time 8000.000 WARNING: Incomplete frame: nr 40397 time 8079.4 --

[gmx-users] problem with grompp (that is used instead of tpbconv)

Hi David, I did what you suggested but encountered with a problem similar to one encountered by tpbconv command. I got the following error: Reading frame 4 time 8000.000 WARNING: Incomplete frame: nr 40397 time 8079.4 --- Program grompp,

Re: [gmx-users] problem about rmsd

dear sudheer, On Fri, 21 Mar 2008, Justin A. Lemkul wrote: Quoting sudheer babu <[EMAIL PROTECTED]>: Thanks for your reply, I am mentioning commands, from crashing the simulation 1. tpbconv -f protein.trr -s protein.tpr -e protein.edr -n index.ndx -o out.tpr You didn't tell tpbconv how

Re: [gmx-users] problem about rmsd

Quoting sudheer babu <[EMAIL PROTECTED]>: > Thanks for your reply, > I am mentioning commands, from crashing the simulation > 1. tpbconv -f protein.trr -s protein.tpr -e protein.edr -n index.ndx -o > out.tpr You didn't tell tpbconv how long to continue the simulation. Use tpbconv -until 1000

[gmx-users] problem about rmsd

Thanks for your reply, I am mentioning commands, from crashing the simulation 1. tpbconv -f protein.trr -s protein.tpr -e protein.edr -n index.ndx -o out.tpr 2.mdrun -v -deffnm -o out.tpr 3.trjcat -f 633ps_pro.xtc 1ns_pro.xtc -settime -o it asked time I mentioned 0 and 633, then it shown that

Re: [gmx-users] changing the time step with tpbconv

OZGE ENGIN wrote: Thank you David, for your quick reply. However, I could not understand the reason why I have to turn on unconstrained_start option. That is if you want to do a continuation simulation. If the continuity is not an issue you can leave it off. -Original Message- From:

Re: [gmx-users] problem about rmsd

Quoting sudheer babu <[EMAIL PROTECTED]>: > Hi all, > I gave 1ns run production step without velocities in md.mdp file, in between > my simulation crashed, so I used *tpbconv for continue that crashed run , > After finishing that I used *trjcat for catenation of my 2 simulation > trajectory files,

[gmx-users] popc

You are experiencing problems because popc is not a protein and pdb2gmx is currently only set up for proteins. More importantly, you already have popc.itp so you don't need to run pdb2gmx on it. I suggest that you read the manual more closely about setting up a simulation and clarify your

Re: Re: [gmx-users] changing the time step with tpbconv

Thank you David, for your quick reply. However, I could not understand the reason why I have to turn on unconstrained_start option. -Original Message- From: David van der Spoel <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Date: Fri, 21 Mar 2008 17:03:06 +0100 Subject: Re

[gmx-users] problem about rmsd

Hi all, I gave 1ns run production step without velocities in md.mdp file, in between my simulation crashed, so I used *tpbconv for continue that crashed run , After finishing that I used *trjcat for catenation of my 2 simulation trajectory files, its shown only 900ps trajectory files into trjout.xt

Re: [gmx-users] changing the time step with tpbconv

OZGE ENGIN wrote: Hi all, I am performing an 80-ns simulation. During the optimization of the parameters that were used in this run, I had performed some small test simulations, and used short frequency values to write the velocities. Unfortunately, I did not change this value into a bigger one

[gmx-users] changing the time step with tpbconv

Hi all, I am performing an 80-ns simulation. During the optimization of the parameters that were used in this run, I had performed some small test simulations, and used short frequency values to write the velocities. Unfortunately, I did not change this value into a bigger one before starting t

Re: [gmx-users] popc

Quoting Chiara Parravicini <[EMAIL PROTECTED]>: > Thank you for your advice! > I reformatted the ffG43a2x.hdb file, but now pdb2gmx is complaining about > the ffG43a2x-n.tdb file, that is different from the ffG53a6 one, and > probably it would complain also for ffG43a2x-c.tdb. Here, also the field

Re: [gmx-users] popc

Thank you for your advice! I reformatted the ffG43a2x.hdb file, but now pdb2gmx is complaining about the ffG43a2x-n.tdb file, that is different from the ffG53a6 one, and probably it would complain also for ffG43a2x-c.tdb. Here, also the fields gd_* don't match. Is there the way to use the existing

Re: [gmx-users] popc

Quoting Chiara Parravicini <[EMAIL PROTECTED]>: > Dear gromacs users, > > I would like to perform simulations of a protein embedded in popc, using a > force field of the gromos series and I downloaded popc.pdb, popc.itp, > lipid.itpa and the force field ffG43a2x extended for lipids. > Looking th

[gmx-users] popc

Dear gromacs users, I would like to perform simulations of a protein embedded in popc, using a force field of the gromos series and I downloaded popc.pdb, popc.itp, lipid.itpa and the force field ffG43a2x extended for lipids. Looking throughout the archive I found different suggestions, but none

Re: [gmx-users] information about tau_p

pragya chohan wrote: Hi users Can you please tell me if in an anisotropic pressure coupling type the diagonal pau_p should be 0 or not. And how it can affect our simulation. What I mean is: I have ref_p = 1.0 1.0 1.0 0 0 0 With that is it better to use tau_p= 1.0 1.0 1.0 0 0 0 or tau_p =1 1

[gmx-users] information about tau_p

Hi users Can you please tell me if in an anisotropic pressure coupling type the diagonal pau_p should be 0 or not. And how it can affect our simulation. What I mean is: I have ref_p = 1.0 1.0 1.0 0 0 0 With that is it better to use tau_p= 1.0 1.0 1.0 0 0 0 or tau_p =1 1 1 1 1 1 and please tel

Re: [gmx-users] Problem about tpbconv

> Hi all, > I am runnning system with 1ns NVT production step without velocities in > md.mdp file, inbetween the simulation was crashed because power problem > and > I want continue the run from where it was stopped by using *tpbconv but it > shown warning, fatal error and finally stopped without g