Re: [gmx-users] the growth of the molecule

2014-09-23 Thread Jakub Krajniak
W dniu 22.09.2014 o 16:45, Александр Селютин pisze: Thanks to everyone I have idea that I can stop simulation, change topology(move end of molecule, add new atoms) and start again. It should be repeated every 2 ps. But it can be very slowly. Does anybody know how to do it more correctly?

[gmx-users] Electrostatic energy between two groups of atoms

2014-09-23 Thread h . alizadeh
Dear users, Can we calculate electrostatic energy between two groups of atoms in GROMACS? Best wishes, H.A -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] non-bonded F kernel

2014-09-23 Thread xiexiao...@sjtu.edu.cn
I used the command mdrun_mpi -v -deffnm test to run the .tpr file and find some new information in my log file: GPU timings - Computing: Count Wall t (s) ms/step %

[gmx-users] TIGER2 implementation in GROMACS

2014-09-23 Thread João Henriques
Dear all, Short and fast: I'm interested in using/testing the TIGER2*** method, currently implemented in NAMD, but I'm what you would call a GROMACS person. Are there any plans to implement it for GROMACS in the near future? Is this something that has been discussed among the developers at some

Re: [gmx-users] Electrostatic energy between two groups of atoms

2014-09-23 Thread Justin Lemkul
On 9/23/14 7:36 AM, h.aliza...@znu.ac.ir wrote: Dear users, Can we calculate electrostatic energy between two groups of atoms in GROMACS? energygrps in the .mdp file. Whether or not that quantity means anything (if using PME, for instance) is another matter and depends to some extent on

Re: [gmx-users] TIGER2 implementation in GROMACS

2014-09-23 Thread Mark Abraham
Hi, I don't know of anyone with such plans. It wouldn't be hard for the right person, but that goes for dozens of things such a person could do... :-) Mark On Tue, Sep 23, 2014 at 1:46 PM, João Henriques joao.henriques.32...@gmail.com wrote: Dear all, Short and fast: I'm interested in

Re: [gmx-users] TIGER2 implementation in GROMACS

2014-09-23 Thread João Henriques
Ok, I see what you mean. Thanks anyway. Best regards, João On Tue, Sep 23, 2014 at 1:49 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, I don't know of anyone with such plans. It wouldn't be hard for the right person, but that goes for dozens of things such a person could do... :-)

Re: [gmx-users] TIGER2 implementation in GROMACS

2014-09-23 Thread João M . Damas
I guess you'll have to become a NAMD person ;-) On Tue, Sep 23, 2014 at 2:22 PM, João Henriques joao.henriques.32...@gmail.com wrote: Ok, I see what you mean. Thanks anyway. Best regards, João On Tue, Sep 23, 2014 at 1:49 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, I

[gmx-users] g_dos -n

2014-09-23 Thread xy21hb
hi all, why cannot g_dos accept -n as supposed? and g_dos normally gives very sharp curve, any thoughts on that? P.S. I use 2 fs to integrate a typical protein-water system. Thanks, Yao -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Compile and Run on Xsede

2014-09-23 Thread Johnny Lu
Hi. On stampede of xsede.org https://portal.xsede.org/tacc-stampede, I compiled cmake, and then gromacs 4.6.7 with and without gpu, with the following cmake configuration: without gpu: module load mkl module load cuda/6.0 module load mvapich2 export MKLROOT=$TACC_MKL_DIR export

Re: [gmx-users] Compile and Run on Xsede

2014-09-23 Thread Justin Lemkul
On 9/23/14 12:45 PM, Johnny Lu wrote: Hi. On stampede of xsede.org https://portal.xsede.org/tacc-stampede, I compiled cmake, and then gromacs 4.6.7 with and without gpu, with the following cmake configuration: without gpu: module load mkl module load cuda/6.0 module load mvapich2 export

[gmx-users] conversion of the AMBER parameters to GROMACS with negative barrier height values

2014-09-23 Thread ABEL Stephane 175950
Hello all, I am trying to convert some GLYCAM parameters to do simulations with the GROMACS code. In the glycam force field, several dihedral terms have negative barrier height values, for instance, -20 in the following parameter: Os-Cj-Cj-Ha 1 -20.00 0.0 2

Re: [gmx-users] I: How to rolled up a polymer chain

2014-09-23 Thread Mohd Farid Ismail
Can I ask you something. What do you mean by rolled up? Do you mean create the tangled conformation of polymer chains? --Farid 22.09.2014, 20:46, marcello cammarata mstaxmarce...@yahoo.it: Hi,  i had checked all the archives, i have read about 100posts in the last 2 month. Nobody have

Re: [gmx-users] conversion of the AMBER parameters to GROMACS with negative barrier height values

2014-09-23 Thread Justin Lemkul
On 9/23/14 1:18 PM, ABEL Stephane 175950 wrote: Hello all, I am trying to convert some GLYCAM parameters to do simulations with the GROMACS code. In the glycam force field, several dihedral terms have negative barrier height values, for instance, -20 in the following parameter:

Re: [gmx-users] I: How to rolled up a polymer chain

2014-09-23 Thread marcello cammarata
yes, i need yto know how it go to tangled, related with the lenght of chain, the number of chains in volume unit. For now the problem is that when i run pdd2gmx, i don't choose any solvent, because there isn't eny solvent, i choose only a kind of force field present in the database software.

[gmx-users] g_dos -n

2014-09-23 Thread xy21hb
hi all, I wonder why g_dos cannot accept -n as supposed? and why g_dos normally gives very sharp curve, any thoughts on that? P.S. I use 2 fs to integrate a typical protein-water system. Thanks, Yao -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Compile and Run on Xsede

2014-09-23 Thread Johnny Lu
It works now. I didn't know there are gpudev and gpu queues. Have to use those to run cuda programs. There are 3 gpu per node... i loaded the correct intel version and then the one without cuda ran ok. On Tue, Sep 23, 2014 at 1:07 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/23/14 12:45

Re: [gmx-users] I: How to rolled up a polymer chain

2014-09-23 Thread marcello cammarata
Do you know how change force field? how i can do this? so the goal can be this, i can consider two molecules asmetilene or ethilene or butene, and i want kwon by appling a set of force field the mutual distance beetween the two groups. How i can do this? how is possible to set force field?

Re: [gmx-users] conversion of the AMBER parameters to GROMACS with negative barrier height values

2014-09-23 Thread Tamir Dingjan
Hi, I've been working with GLYCAM parameters in Gromacs by converting them into Gromacs format using Acpype: https://code.google.com/p/acpype/ . I haven't compared the single-point energy with Amber, but the Gromacs-formatted output is perfectly usable. Regards, Tamir -- Gromacs Users mailing

Re: [gmx-users] I: How to rolled up a polymer chain

2014-09-23 Thread Justin Lemkul
On 9/23/14 7:43 PM, marcello cammarata wrote: Do you know how change force field? how i can do this? Everything you need to create the polymer is described here: http://www.gromacs.org/Documentation/How-tos/Polymers The page includes a link to a discussion that goes step-by-step through

Re: [gmx-users] Commands to run simulations using multiple GPU's in version 5.0.1

2014-09-23 Thread Johnny Lu
Try -nt, -ntmpi, -ntomp, -np (one at a time) ? I forget about what I tried now But I just stop the mdrun, and then read the log file. Also can look for the mdrun page in the offical manual (pdf) and try this page: http://www.gromacs.org/Documentation/Gromacs_Utilities/mdrun?highlight=mdrun

Re: [gmx-users] Different energies of GPU and CPU-only runs with Gromacs 5.x

2014-09-23 Thread Johnny Lu
hi. can i get a link to the redmine issue? I decided to install 4.6.7 instead of 5.0.1 because of this. On Mon, Sep 22, 2014 at 5:52 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Mon, Sep 22, 2014 at 11:02 AM, Machtens, Jan-Philipp j.macht...@fz-juelich.de wrote: Thanks for the

[gmx-users] log file question

2014-09-23 Thread xiexiao...@sjtu.edu.cn
I used the command mdrun_mpi -v -deffnm test to run the .tpr file and find some new information in my log file: GPU timings - Computing: Count Wall t (s) ms/step %

[gmx-users] which item is gpu wait for cpu?

2014-09-23 Thread xiexiao...@sjtu.edu.cn
I think that the items (wait GPU nonlocal) and (wait GPU local) in log file are the time consuming that cpu wait for gpu. And Does anyone know that which item is the time consuming that gpu wait for cpu in log file? xiexiao...@sjtu.edu.cn -- Gromacs Users mailing list * Please search the

Re: [gmx-users] Commands to run simulations using multiple GPU's in version 5.0.1

2014-09-23 Thread Siva Dasetty
Thank you Lu for the reply. As I have mentioned in the post, I have already tried those options but it didn't work. Kindly please let me know if you have anymore suggestions. Thank you, On Tue, Sep 23, 2014 at 8:41 PM, Johnny Lu johnny.lu...@gmail.com wrote: Try -nt, -ntmpi, -ntomp, -np (one

[gmx-users] How can I select a group number automatically

2014-09-23 Thread Xiaobin Cao
Hi Gromacs users, When I do msd analysis (g_msd), there is a promotion to select a group number. I am wondering how can I select a number using a script. So the computer can do analysis automatically. Thank you. _ Xiaobin Cao Dept of Geology

Re: [gmx-users] How can I select a group number automatically

2014-09-23 Thread Chandan Choudhury
Use echo $echo 0 | g_msd -s topol.tpr -f traj.xtc Chandan On Wed, Sep 24, 2014 at 9:35 AM, Xiaobin Cao x...@lsu.edu wrote: Hi Gromacs users, When I do msd analysis (g_msd), there is a promotion to select a group number. I am wondering how can I select a number using a script. So the