Re: [gmx-users] add Mn in itp file

2014-10-23 Thread andrea
Hi, have look here in the supp mat. of this paper: http://onlinelibrary.wiley.com/doi/10.1002/anie.201202032/abstract Mn2+ for OPLS ff in case you needed it best and On 22/10/2014 16:13, Justin Lemkul wrote: On 10/22/14 5:09 AM, yaser wrote: hi i tried add Mn in .itp file but its need

Re: [gmx-users] Implementation of SHAKE

2014-10-23 Thread Mario Fernández Pendás
Hi Mark, There was something in the matrix calculations that was not totally clear to me. That is why I started to think in a different approach. Now everything is fine. Thank you very much, Mario Fernández-Pendás El 23/10/2014 01:15, Mark Abraham mark.j.abra...@gmail.com escribió: Hi, No,

Re: [gmx-users] Accelerated MD

2014-10-23 Thread Patrick Fuchs
Hi Doug, I recently read a good review on ABF http://pubs.acs.org/doi/abs/10.1021/jp506633n. It's focused on ABF but there's a section which compares ABF to other techniques. While I'm at it, are there any plans from gromacs devs to implement ABF in gromacs? Best, Patrick Le 20/10/2014

[gmx-users] how can i install sse4.1 and avx_256

2014-10-23 Thread Yaser Hosseini
hi Reading file md.tpr, VERSION 4.6.5 (single precision) Using 4 MPI threads Compiled acceleration: SSE4.1 (Gromacs could use AVX_256 on this machine, which is better) how can i use this features for better mdrun speed. thanke you. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] how to generate executable file g_energy_mpi ?

2014-10-23 Thread Vinson Leung
Hi everyone. I am new to Gromacs and have some question in the building part. I can only genarate mdrun_mpi when set the DGMX_BUILD_MDRUN_ONLY to ON and when I set it to OFF, it can only produce gmx_mpi and template in the bin directory. What is the different between mdrun_mpi and gmx_mpi ?

Re: [gmx-users] how can i install sse4.1 and avx_256

2014-10-23 Thread Milan Melicherčík
Hello, you need to recompile Gromacs with -DGMX_SIMD=AVX_256 flag. Or not set it and cmake should detect and use the best version automatically. http://www.gromacs.org/Documentation/Installation_Instructions_4.6 Cheers. Milan On Thursday 23 October 2014 13:32:31 Yaser Hosseini wrote: hi

Re: [gmx-users] how to generate executable file g_energy_mpi ?

2014-10-23 Thread Justin Lemkul
On 10/23/14 6:37 AM, Vinson Leung wrote: Hi everyone. I am new to Gromacs and have some question in the building part. I can only genarate mdrun_mpi when set the DGMX_BUILD_MDRUN_ONLY to ON and when I set it to OFF, it can only produce gmx_mpi and template in the bin directory. What is the

Re: [gmx-users] charge group moved too far between two domain decomposition step

2014-10-23 Thread Justin Lemkul
On 10/23/14 1:47 AM, Kester Wong wrote: Thanks for the input Mark, Hi Mark, Thanks for the input, I thought a time step of 2 fs is small enough? Not always for unconstrained bonds. The largest stable time step is determined by the size of the period of the

Re: [gmx-users] how can i install sse4.1 and avx_256

2014-10-23 Thread Justin Lemkul
On 10/23/14 6:02 AM, Yaser Hosseini wrote: hi Reading file md.tpr, VERSION 4.6.5 (single precision) Using 4 MPI threads Compiled acceleration: SSE4.1 (Gromacs could use AVX_256 on this machine, which is better) how can i use this features for better mdrun speed. The level of optimization

Re: [gmx-users] how to generate executable file g_energy_mpi ?

2014-10-23 Thread Vinson Leung
and how can I get those analysis tools? On Thu, Oct 23, 2014 at 7:31 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/23/14 6:37 AM, Vinson Leung wrote: Hi everyone. I am new to Gromacs and have some question in the building part. I can only genarate mdrun_mpi when set the

Re: [gmx-users] how to generate executable file g_energy_mpi ?

2014-10-23 Thread Justin Lemkul
On 10/23/14 7:48 AM, Vinson Leung wrote: and how can I get those analysis tools? http://www.gromacs.org/Documentation/Installation_Instructions Everything gets built by default unless you use -DGMX_BUILD_MDRUN_ONLY=ON -Justin On Thu, Oct 23, 2014 at 7:31 PM, Justin Lemkul

Re: [gmx-users] how to generate executable file g_energy_mpi ?

2014-10-23 Thread Justin Lemkul
On 10/23/14 8:03 AM, Vinson Leung wrote: But I remove the option -DGMX_BUILD_MDRUN_ONLY=ON and can only get gmx_mpi and template. There is no those analysis tools and my Gromacs version is 5.0.2. My build congfiure is like below:

Re: [gmx-users] how to generate executable file g_energy_mpi ?

2014-10-23 Thread Vinson Leung
Thanks. It seem to much more clear for me:). I have compiled again with -DGMX_MPI=OFF. Now I have only two executable file (gmx and template) in the bin dir. If I want to generate .xvg file and I already have .edr file. What is the comand line exactly ? Vincent On Thu, Oct 23, 2014 at 8:05 PM,

Re: [gmx-users] how to generate executable file g_energy_mpi ?

2014-10-23 Thread Justin Lemkul
On 10/23/14 8:26 AM, Vinson Leung wrote: Thanks. It seem to much more clear for me:). I have compiled again with -DGMX_MPI=OFF. Now I have only two executable file (gmx and template) in the bin dir. If I want to generate .xvg file and I already have .edr file. What is the comand line exactly

Re: [gmx-users] how to generate executable file g_energy_mpi ?

2014-10-23 Thread Vinson Leung
Thank you very much:) It help me a lot ! Best Vincent On Thu, Oct 23, 2014 at 8:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/23/14 8:26 AM, Vinson Leung wrote: Thanks. It seem to much more clear for me:). I have compiled again with -DGMX_MPI=OFF. Now I have only two executable

[gmx-users] binding Free energy

2014-10-23 Thread Urszula Uciechowska
Dear gromacs user, I would like to calculate Binding Free Energy Calculations for my protein-DNA complex (already run for 50ns). Is there any manual or tutorial (for more complex systems) available? best regards Urszula - Ta wiadomość została wysłana z

Re: [gmx-users] binding Free energy

2014-10-23 Thread Justin Lemkul
On 10/23/14 10:35 AM, Urszula Uciechowska wrote: Dear gromacs user, I would like to calculate Binding Free Energy Calculations for my protein-DNA complex (already run for 50ns). Is there any manual or tutorial (for more complex systems) available? See published methods like g_mmpbsa (very

Re: [gmx-users] binding Free energy

2014-10-23 Thread Erik Marklund
Dear Urszula, Apologies for the self promotion, but we've made some attempts to do that for a TF-DNA complex: http://www.pnas.org/content/110/49/19796. Note that the rotational degrees of freedom are hard to sample and you may need some further assumptions about mesoscopic scales for the

Re: [gmx-users] binding Free energy

2014-10-23 Thread andrea
Hi, thanks Justin to point out our tool GMXPBSA (GMXAPBS was the old one) http://www.sciencedirect.com/science/article/pii/S0010465514002240 and new version 2.1: http://www.sciencedirect.com/science/article/pii/S0010465514003154 The link to the program is still not avaliable but you can

[gmx-users] Question

2014-10-23 Thread Eric Smoll
Hello Gromacs users, If I have all the files that were used to generate a trajectory file, what is the proper procedure to update the atomnames in the trajectory. My best guess is below. Is this problematic? # remove first frame of trajectory cat EOF tmp.ndx [ FIRSTFRAME ] 1 EOF trjconv -fr

Re: [gmx-users] Question

2014-10-23 Thread Justin Lemkul
On 10/23/14 4:29 PM, Eric Smoll wrote: Hello Gromacs users, If I have all the files that were used to generate a trajectory file, what is the proper procedure to update the atomnames in the trajectory. My best guess is below. Is this problematic? # remove first frame of trajectory cat EOF

Re: [gmx-users] Question

2014-10-23 Thread Eric Smoll
Thanks for the guidance, Justin. -Eric On Thu, Oct 23, 2014 at 2:39 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/23/14 4:29 PM, Eric Smoll wrote: Hello Gromacs users, If I have all the files that were used to generate a trajectory file, what is the proper procedure to update the

[gmx-users] error in the middle of running mdrun_mpi

2014-10-23 Thread Nizar Masbukhin
Dear gromacs users, I try simulate protein folding using REMD sampling method in implicit solvent. I run my simulation on MPI-compiled gromacs 5.0.2 on single node. I have succesfully minimized equilibrated (NVT-constrained, and NPT constrained) my system. However, In the middle of mdrun_mpi

Re: [gmx-users] error in the middle of running mdrun_mpi

2014-10-23 Thread Mark Abraham
Hi, The warning message told you not to increase the table distance unless you were sure the table distance was the problem. Why were you sure the table distance was the problem, rather than some form of general instability of your system? In addition to all the usual reasons for

Re: [gmx-users] charge group moved too far between two domain decomposition step

2014-10-23 Thread Kester Wong
Hi Justin and all, Thanks for the input, I thought a time step of 2 fs is small enough? Not always for unconstrained bonds. The largest stable time step is determined by the size of the period of the fastest oscillation, which is vibrations of bonds to

Re: [gmx-users] charge group moved too far between two domain decomposition step

2014-10-23 Thread Justin Lemkul
On 10/23/14 10:19 PM, Kester Wong wrote: Hi Justin and all, Thanks for the input, I thought a time step of 2 fs is small enough? Not always for unconstrained bonds. The largest stable time step is determined by the size of the period of the