[gmx-users] polymer in octahedron box pbc problem

2015-10-01 Thread gromacs query
Hi All, I have linear polymer in octahedron box and when I try to visualise a polymer in octahedraon box then water octahedron box looks as expected but my polymer looks broken. trjconv_avx -f input.xtc -o out.xtc -pbc mol -ur compact -s input.tpr -b 10 I have tried to use -center (whole

Re: [gmx-users] colleague subscribed to gromacs mailing list but unable to get replies

2015-10-01 Thread Justin Lemkul
On 10/1/15 3:09 AM, Raag Saluja wrote: Hi! A colleague of mine is having a little problem with the gromacs mailing list. She says she subscribed to it, but when she posts, she gets no reply. She does get the digest, however. She asked me to ask you if you could kindly help her. Use the

Re: [gmx-users] Atom OXT in PHE

2015-10-01 Thread Justin Lemkul
On 9/30/15 1:06 PM, Sepideh Kavousi wrote: Hi, In the force fiels that you use this atom in not introduced. you have to import the information of atom in the atomtypes.atp file in the related force field you use The error is not at all related to the content of atomtypes.atp. The problem

[gmx-users] Peptide, lipid simulation

2015-10-01 Thread badamkhatan togoldor
Dear Gromacs Users,I would like to use g_membed to insert my peptide into membrane. But I got this errors and notes in grompp ERROR 1 [file membed.mdp]:   Energy group exclusions are not (yet) implemented for the Verlet scheme NOTE 4 [file membed.mdp]:   NVE simulation with an initial

Re: [gmx-users] colleague subscribed to gromacs mailing list but unable to get replies

2015-10-01 Thread David van der Spoel
On 01/10/15 09:09, Raag Saluja wrote: Hi! A colleague of mine is having a little problem with the gromacs mailing list. She says she subscribed to it, but when she posts, she gets no reply. She does get the digest, however. She asked me to ask you if you could kindly help her. Have her go to

Re: [gmx-users] Insert molecules in system with minimum distance between them

2015-10-01 Thread Justin Lemkul
On 9/30/15 12:15 PM, Ebert Maximilian wrote: Dear list, I am trying to add n-number of molecules in my prepare protein+water+ions box but keep a minimum distance of 1 nm in all directions between the newly inserted molecules. On top of that I want to replace solvent molecules with the

Re: [gmx-users] polymer in octahedron box pbc problem

2015-10-01 Thread Victor Rosas Garcia
Have you tried the option "-pbc whole" instead of "-pbc mol"? Victor 2015-10-01 6:43 GMT-05:00 gromacs query : > Hi All, > > I have linear polymer in octahedron box and when I try to visualise a > polymer in octahedraon box then water octahedron box looks as expected but

Re: [gmx-users] Install Gromacs on VirtualBox

2015-10-01 Thread Szilárd Páll
My guess is that you need to turn off RDTSCP: http://www.gromacs.org/Documentation/Installation_Instructions_5.0#portability-aspects -- Szilárd On Thu, Oct 1, 2015 at 4:36 PM, Simon Dürr wrote: > I have problems installing Gromacs on a VirtualBox machine. > >

Re: [gmx-users] polymer in octahedron box pbc problem

2015-10-01 Thread gromacs query
Hi, I think its solved, I used -center option but now rather selecting full polymer I selected some of the central residue in polymer chain. Now box looks good and polymer is not broken. JIom On Thu, Oct 1, 2015 at 3:43 PM, gromacs query wrote: > Hi Victor, > > With

Re: [gmx-users] How OpenMP works with CUDA/GPU in Gromacs

2015-10-01 Thread Szilárd Páll
Hi, I suggest you check some of our recent papers on the heterogeneous parallelization. Chapter two in the following (GROMACS 4.6-related) paper gives a good overview of the (then) new parallelization aspects like threading and GPU acceleration:

Re: [gmx-users] please help in analysis of picture attached

2015-10-01 Thread Victor Rosas Garcia
this list does not accept attachments. Please upload your file to some file-sharing service and tell us the link. Victot 2015-10-01 2:21 GMT-05:00 surbhi mahajan : > Hi, > I am trying to do simulations using lipids like DPPC and DMPC , i am not > able to develop a

Re: [gmx-users] Gromacs GPU got hang

2015-10-01 Thread Szilárd Páll
The only way to know more is to either attach a debugger to the hanging process or possibly with an ltrace/strace to see in which library or syscalls is the process hanging. I suggest you try attaching a debugger and getting a stack trace (see

[gmx-users] Install Gromacs on VirtualBox

2015-10-01 Thread Simon Dürr
I have problems installing Gromacs on a VirtualBox machine. Stats of the System: Lubuntu 32bit, 14.04 LTS build-essential and cmake are installed. I follow the instructions: > tar xfz gromacs-5.0.6.tar.gz > cd gromacs-5.0.6 > mkdir build > cd build > cmake .. -DGMX_BUILD_OWN_FFTW=ON

Re: [gmx-users] Error in gromacs-5.1 installation

2015-10-01 Thread Szilárd Páll
Hi, Can you please open an issue on redmine.gromacs.org and attach your CMakeCache.txt file to the issue. To work around the issue, you'll likely have to disable NVML support which ATM requires removing all lines that start with "NVML_" from your CMakeCache file. Cheers, -- Szilárd On Tue,

Re: [gmx-users] polymer in octahedron box pbc problem

2015-10-01 Thread gromacs query
Hi Victor, With 'pbc whole' polymer remains broken in pbc and the octahedron box looks weird too. JIom On Thu, Oct 1, 2015 at 2:52 PM, Victor Rosas Garcia wrote: > Have you tried the option "-pbc whole" instead of "-pbc mol"? > > Victor > > 2015-10-01 6:43 GMT-05:00

Re: [gmx-users] GPU+CPU

2015-10-01 Thread Szilárd Páll
On Sun, Sep 20, 2015 at 7:11 PM, Parker de Waal wrote: > Hello Everyone, > > I recently started to explore GROMACS (switching over from AMBER) and need > some help understanding how to launch GPU+CPU simulations. > > GROMACS 5.0.6 was compiled with the following cmake

Re: [gmx-users] frequent stop of GPU jobs at specific simulation steps.

2015-10-01 Thread Szilárd Páll
TL; DR If you want to investigate the issue further check my reply here: http://comments.gmane.org/gmane.science.biology.gromacs.user/80120 -- Szilárd On Mon, Sep 28, 2015 at 5:34 AM, Zhongjin He wrote: > Dear GMX users, > > > Recently I encountered a strange problem in using

Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

2015-10-01 Thread Szilárd Páll
On Thu, Oct 1, 2015 at 8:01 AM, Venkat Reddy wrote: > Hi > Gromacs-5.1 version can not read xtc files. However, it can access single > frame gro/pdb files. > That's a bold claim that IMO requires equally strong proof. In your other mail to the list you were talking about a

Re: [gmx-users] Peptide, lipid simulation

2015-10-01 Thread Justin Lemkul
On 10/1/15 9:07 AM, badamkhatan togoldor wrote: Dear Gromacs Users,I would like to use g_membed to insert my peptide into membrane. But I got this errors and notes in grompp ERROR 1 [file membed.mdp]: Energy group exclusions are not (yet) implemented for the Verlet scheme NOTE 4 [file

Re: [gmx-users] Install Gromacs on VirtualBox

2015-10-01 Thread Simon Dürr
I used this: > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=OFF > -DGMX_USE_RDTSCP=OFF But Still: Test project /home/simon/gromacs-5.0.6/build Start 1: TestUtilsUnitTests 1/15 Test #1: TestUtilsUnitTests ...***Exception: Illegal 0.29 sec Start 2:

Re: [gmx-users] Martini domain decomposition problem

2015-10-01 Thread Szilárd Páll
Hi Gábor, Without more details (and little experience with martini systems) I can suggest: tweaking DD so you don't end up with a too small box wrt the number of cells by: - Changing the number of ranks by using less/more cores to get a convenient decomposition; I assume you had 6x4x4 before on

[gmx-users] Query regarding exclusions and Coulomb-SR energies

2015-10-01 Thread Siva Dasetty
Dear all, As the Verlet cut-off scheme does not support energygrp-excl parameter yet, we are looking for an alternative to exclude all non bonded interactions between the frozen atoms. The gromacs manual (section 5.4) states that all the non bonded interactions between the pairs in the [

[gmx-users] GMXLIB does not induce residuetype.dat

2015-10-01 Thread Ebert Maximilian
Dear list, I have my own force field working folder so I cloned the entire top folder to no mess with the original files. I added residues to the residue type file to add my residues to the protein group. My FF is included due to the GMXLIB environmental variable but my modified

[gmx-users] Query regarding exclusions and Coulomb-SR energies

2015-10-01 Thread Siva Dasetty
Dear all, As the Verlet cut-off scheme does not support energygrp-excl parameter yet, we are looking for an alternative to exclude all non bonded interactions between the frozen atoms. The gromacs manual (section 5.4) states that all the non bonded interactions between the pairs in the [

[gmx-users] colleague subscribed to gromacs mailing list but unable to get replies

2015-10-01 Thread Raag Saluja
Hi! A colleague of mine is having a little problem with the gromacs mailing list. She says she subscribed to it, but when she posts, she gets no reply. She does get the digest, however. She asked me to ask you if you could kindly help her. -- Regards, Raag -- Gromacs Users mailing list *

Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

2015-10-01 Thread Venkat Reddy
Hi Gromacs-5.1 version can not read xtc files. However, it can access single frame gro/pdb files. On Thu, Oct 1, 2015 at 10:44 AM, Teemu Murtola wrote: > Are you saying that you cannot open any xtc files? If that is the case, > then this may not have anything to do

[gmx-users] please help in analysis of picture attached

2015-10-01 Thread surbhi mahajan
Hi, I am trying to do simulations using lipids like DPPC and DMPC , i am not able to develop a coarse grained model nor am i able to understand the purpose of the bead that i have got from SBCG model . Please help me in analyzing this attachment. I am very new to this field. please help Regards

[gmx-users] Free Energy of Liquid Water

2015-10-01 Thread Nathan K Houtz
Hi everyone, I would like to use Gromacs to do Thermodynamic Integration (TI) from liquid water (TIP4P model) to an ideal gas, to find the relative free energy. To do this, I believe one generally integrates above the critical point by increasing the temperature above the critical temperature

[gmx-users] vdw modifier and coulomb modifier

2015-10-01 Thread Parvez Mh
Dear all, What does vdw and coulomb modifier do in simulation?. Does these option affect simulation accuracy. I did not find these term in literature or any book, why did gromacs introduce these option? Thanks Masrul -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

2015-10-01 Thread Teemu Murtola
Hi, On Thu, Oct 1, 2015 at 6:30 PM Szilárd Páll wrote: > On Thu, Oct 1, 2015 at 8:01 AM, Venkat Reddy wrote: > > Gromacs-5.1 version can not read xtc files. However, it can access single > > frame gro/pdb files. > > > > That's a bold claim that IMO

Re: [gmx-users] distance dependent energy

2015-10-01 Thread Cuong Nguyen
Thank you Mark and Erik, Van On Wednesday, 23 September 2015, Mark Abraham wrote: > Hi, > > On Tue, Sep 22, 2015 at 5:47 PM Cuong Nguyen > wrote: > > > Dear Gromacs users, > > > > I would like to work out the energy (total and

Re: [gmx-users] Simulations of proteins in membrane bilayer

2015-10-01 Thread Catarina A. Carvalheda dos Santos
Hey, If that doesn't do the trick use the flags suggested by Terry and also '-ur compact'. This works for me. Regards, On 1 October 2015 at 02:49, Terry wrote: > Hi, > > Try options '-pbc mol -center' with the gmx trjconv tool. > > Terry > > > On Thu, Oct 1, 2015 at

[gmx-users] protein simulation

2015-10-01 Thread elham tazikeh
Dear GMX users i want to compare binding free energy between experimental and MD computations In experimental methods, we assumed that all atoms of a protein that binding to ligand, butin MD simulations, we just assume the sections of subdomain(s) that binds to ligand Is this way correct to