[gmx-users] a question on energygrps

2013-07-14 Thread Albert
Hello: I've got a question on energygrps options in .mdp file. This option is usually used for establishing the groups for the energy output. I am going to study the entropy changes of protein-ligand-SOL in a membrane system, I am just wondering shall I specify each compoenent in

[gmx-users] Restraints influeincing free energy calculations

2013-07-14 Thread Nash, Anthony
Hi all, Just a quick question - and perhaps some wisdom from those with more experience. I am trying to use metadynamics with gromacs to plot an energy landscape about the rotation of two proteins. If I were to define my collective variables as ThetaA and ThetaB, Theta being the rotation about

Re: [gmx-users] a question on energygrps

2013-07-14 Thread Justin Lemkul
On 7/14/13 6:21 AM, Albert wrote: Hello: I've got a question on energygrps options in .mdp file. This option is usually used for establishing the groups for the energy output. I am going to study the entropy changes of protein-ligand-SOL in a membrane system, I am just wondering shall I

[gmx-users] qm-mm calculation

2013-07-14 Thread Nilesh Dhumal
Hello, I am trying to run the qm-mm gas phase calculations for my system. I am using following in md.mdp file. title = cpeptide MD cpp = /usr/bin/cpp integrator = md dt = 0.001; ps ! nsteps = 500 ; total 5 ps.

[gmx-users] How to compile Cygwin 4.6.3 for Windows using Cygwin

2013-07-14 Thread bhf70
Hello, How to compile Cygwin 4.6.3 for Windows using Cygwin ? I did so: tar xfz gromacs-4.6.tar.gz cd gromacs-4.6 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON (fftw 3.3 - install) make Error message Thank you. -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] qm-mm calculation

2013-07-14 Thread Justin Lemkul
On 7/14/13 11:36 AM, Nilesh Dhumal wrote: Hello, I am trying to run the qm-mm gas phase calculations for my system. I am using following in md.mdp file. title = cpeptide MD cpp = /usr/bin/cpp integrator = md dt = 0.001; ps !

Re: [gmx-users] How to compile Cygwin 4.6.3 for Windows using Cygwin

2013-07-14 Thread Justin Lemkul
On 7/14/13 1:04 PM, bh...@udsu.ru wrote: Hello, How to compile Cygwin 4.6.3 for Windows using Cygwin ? I did so: tar xfz gromacs-4.6.tar.gz cd gromacs-4.6 The version 4.6 tarball will not give you version 4.6.3 :) Unless this is a typo, make sure you're actually working with the

Re: [gmx-users] How to compile Cygwin 4.6.3 for Windows using Cygwin

2013-07-14 Thread bhf70
Error message, аfter the make: In file included from /cygdrive/d/1/gromacs-4.6.3/src/gmxlib/thread_mpi/atomic.c:38:0: /cygdrive/d/1/gromacs-4.6.3/src/gmxlib/thread_mpi/impl.h:504:20: ошибка: field «timer_init» has incomplete type src/gmxlib/CMakeFiles/gmx.dir/build.make:8061: recipe for target

[gmx-users] acidic pH

2013-07-14 Thread fatemeh ramezani
Hello dear users I'm simulating gold nanoparticle interaction with protein. I want to change the pH of system. What would  need to be changed to simulate this system at pH 3.0? thanks you   Fatemeh Ramezani -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] acidic pH

2013-07-14 Thread Justin Lemkul
On 7/14/13 2:23 PM, fatemeh ramezani wrote: Hello dear users I'm simulating gold nanoparticle interaction with protein. I want to change the pH of system. What would need to be changed to simulate this system at pH 3.0? As is discussed frequently on this list (hint: check the archive for

[gmx-users] Cyclic Peptide Topology

2013-07-14 Thread jriedel
Hi, I'm want to run a MD simulation with a Phe-Phe-Phe-Phe-Gly cyclic peptide. But I'm have problems generating the topology files. When I try to use the strategy to generate a topology file for the linear GF using pdb2gmx -ff charmm27 -f pep.pdb -o pep.gro -ter -water spce and choosing None

Re: [gmx-users] Cyclic Peptide Topology

2013-07-14 Thread Justin Lemkul
On 7/14/13 7:07 PM, jriedel wrote: Hi, I'm want to run a MD simulation with a Phe-Phe-Phe-Phe-Gly cyclic peptide. But I'm have problems generating the topology files. When I try to use the strategy to generate a topology file for the linear GF using pdb2gmx -ff charmm27 -f pep.pdb -o

Re: [gmx-users] Figures of PCA analysis

2013-07-14 Thread Ahmet yıldırım
Can anybody help me understand these better? 2013/7/10 lloyd riggs lloyd.ri...@gmx.ch There vectors. Theres some good older papers explaining the whole thing from Van Gunstern, Berendsen, and some other good ones from de Groot that explain them well and includes combining them with other

[gmx-users] Re: extreme projections

2013-07-14 Thread Ahmet yıldırım
any one please help me out with this problem? 2013/7/10 Ahmet yıldırım ahmedo...@gmail.com Dear users, I extracted separate extreme projections using g_anaeig. I have to make pictures which show the difference. Can you help me, someone who makesthem using pymolbefore ? -- Ahmet

[gmx-users] snapshot

2013-07-14 Thread Rama
Hi, How to get a snapshots in equal intervals of time (250ps) from production MD trajectory. I'm using -sep , -t0, -timestep but output came only one .gro file. -- View this message in context: http://gromacs.5086.x6.nabble.com/snapshot-tp5009837.html Sent from the GROMACS Users Forum

Re: [gmx-users] snapshot

2013-07-14 Thread Justin Lemkul
On 7/14/13 9:03 PM, Rama wrote: Hi, How to get a snapshots in equal intervals of time (250ps) from production MD trajectory. I'm using -sep , -t0, -timestep but output came only one .gro file. trjconv -skip -sep should work, but without exact command lines and the output you received (as

RE: [gmx-users] Figures of PCA analysis

2013-07-14 Thread Dallas Warren
Which papers have you read so far? Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a