[gmx-users] Re: Anomaly in Temperature Behavior

S. Alireza B wrote It appears that my solid phase completely melts after 700 ps. Please see the video below. http://www.youtube.com/watch?v=6iidpiivVRIfeature=youtu.be Can I conclude that my solid phase is not really far from the equilibrium as it does not suddenly melt/collapse? Yes, i

Re: [gmx-users] Dynamics of the salt-bridges

Hi, If you don't care about the exact distances, but rather the time the groups spend within a certain distance, g_hbond -contact can be useful. Best, Erik On Feb 3, 2013, at 6:36 PM, James Starlight wrote: Justin, 1 )for example I want to select in index file only all asp, glu and his

[gmx-users] steepest descents followed by conjugated gradient

Hi Justin i see lots of papers perform steepest descent followed by conjugated gradients. My question do i use the .gro output file as input to perform conjugated gradient minimization as shown in the commands below? or do i repeat pdb2gmx, editconf and genbox on the trajectory file

Re: [gmx-users] How to analysis 10 ns from 20 ns simulation

HI, It should read trjconv. And all analysis tools have the -b and -e flags for excluding the start or the end of a trajectory. Erik On Feb 4, 2013, at 7:00 AM, Emanuel Birru wrote: Use trajconv http://manual.gromacs.org/online/trjconv.html -Original Message- From:

[gmx-users] npt error

hi all, i am trying to simulate a polymer in 5.2 nm box using the gromacs45a3 forcefield. the system is highly concentrated with 3400 water molecules. i did energy minimization for 10ps and NVT, NPT simulations for 100 ps during NPT simulation i got the error message as inner product between old

[gmx-users] confusion about pdb file and coordinate.xvg file

Hi all, I am doing simulation of 864 spce water molecules in a cubic box of 3nm length in gromacs-4.55 version. I have generated the trajectory file using trjconv utility in gromacs. Using the trr file used to generate the .pdb file, I have generated the co-ordinates of H atoms of water using

[gmx-users] confusion about pdb file and coordinate.xvg file

Hi all,  I am doing simulation of 864 spce water molecules in a cubic box of 3nm length in gromacs-4.55 version.  I have generated the trajectory file using trjconv utility in gromacs. Using the  trr file used to generate the .pdb file, I have generated the co-ordinates of H atoms of water

Re: [gmx-users] protein-SWCNT md simulation

On 2/4/13 12:21 AM, Atila Petrosian wrote: Dear Justin Thanks for your reply. 2. Create topology for other elements using g_x2top or other external software and convert them to .itp Can I use PRODRG server to creat topology for cnt? Doubtful. PRODRG produces topologies compatible

Re: [gmx-users] steepest descents followed by conjugated gradient

On 2/4/13 4:53 AM, Ruben Cloete wrote: Hi Justin i see lots of papers perform steepest descent followed by conjugated gradients. My question do i use the .gro output file as input to perform conjugated gradient minimization as shown in the commands below? or do i repeat pdb2gmx, editconf and

Re: [gmx-users] npt error

On 2/4/13 5:19 AM, Rajalakshmi.C wrote: hi all, i am trying to simulate a polymer in 5.2 nm box using the gromacs45a3 forcefield. the system is highly concentrated with 3400 water molecules. i did energy minimization for 10ps and NVT, NPT simulations for 100 ps during NPT simulation i got the

Re: [gmx-users] confusion about pdb file and coordinate.xvg file

On 2/4/13 8:06 AM, biki wrote: Hi all, I am doing simulation of 864 spce water molecules in a cubic box of 3nm length in gromacs-4.55 version. I have generated the trajectory file using trjconv utility in gromacs. Using the trr file used to generate the .pdb file, I have generated the

Re: [gmx-users] Error in BlueGene

Hello Cíntia, On 02/01/2013 04:19 PM, Cintia C. Vequi-Suplicy wrote: Hello Ricardo, I tried to decrease the integration time but I got the same error. The system is running fine in my local core. I have two questions: 1) What do you mean by I balance the domain decomposition for the

Re: [gmx-users] Error in BlueGene

Hello David, I think it is the pressure. Because the error starts with the message below. But this only happens in the BlueGene cluster. In my local cluster it is running fine for 60 ns. Thank you, Cintia vol 0.71 imb F 1% vol 0.74 imb F 1% vol 0.73 imb F 1% vol 0.75 imb F 1% vol

[gmx-users] Re: confusion about pdb file and coordinate.xvg file

Thanks Justin for your reply. -- View this message in context: http://gromacs.5086.n6.nabble.com/confusion-about-pdb-file-and-coordinate-xvg-file-tp5005151p5005163.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] system far from the equilibration state

Hi, I am simulating a system of peptide/membrane/water. If my system is far from the equilibration, would that be correct if I use Berendsen pressure coupling for nano seconds to do NPT equilibration and then change it to Parrinello-Rahman to get the true pressure? Anybody may suggest me

[gmx-users] Dummy/ghost atom - regd

Dear Gromacs users, I am planing to have a reference atom(non-bonded) in my system, whose position will not change during simulations and shouldn't feel/exert any force from/on the other atoms(ghost atom). How can I do this in gromacs ? can I set electrostatic and van der

Re: [gmx-users] system far from the equilibration state

On 2/4/13 2:04 PM, Shima Arasteh wrote: Hi, I am simulating a system of peptide/membrane/water. If my system is far from the equilibration, would that be correct if I use Berendsen pressure coupling for nano seconds to do NPT equilibration and then change it to Parrinello-Rahman to get the

Re: [gmx-users] gromacs-4.6.tar.gz installation question

On 2/4/13 3:30 PM, jeela keel wrote: *Dear All, I am trying to install gromacs, I dowloaded **gromacs-4.6.tar.gzftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gzand following the instruction in the following website

[gmx-users] Re: gromacs-4.6.tar.gz installation question

Thank you for your respond but I did not get the respond to my email, I found the answer on-line. I don't know why I am not receiving any email back from the mailing list. Thank you Jeela On Mon, Feb 4, 2013 at 12:30 PM, jeela keel jeel...@gmail.com wrote: *Dear All, I am trying to install

Re: [gmx-users] Protein unfolded after COM pulling

On 2/4/13 9:32 PM, Yun Shi wrote: Hi all, I am pulling one monomer of a tetrameric protein away from the other three monomers with pull_k1 = 1 and pull_rate1 = 0.0005. As shown in the attached picture, the green monomer (being pulled) has unfolded while two regions on it are still

[gmx-users] Membrane simulation - error during EM after inflation step

Hello Justin, Thank you for providing a tutorial for membrane simulation. I am doing membrane simulation by following your tutorial. When I tried to do energy minimization after inflating the system i got the following result. Steepest Descents converged to machine precision in 15 steps, but did

[gmx-users] Regarding manual velocity generation in simulation

Hello All, Please let me know whether is it possible to manually assign the velocity for each atom in the simulation instead of generating through gen_vel option. -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org