Re: [gmx-users] Re: energy conservation: shift vs shifted user potential

On 12/06/2012 9:05 PM, Anja Kuhnhold wrote: Ok, that didn't help me much. Of course I changed both, potential and force to shifted ones. That's not what you said you did with g(x) and h(x)... but whatever. And sure I used a little fortran code to generate the tables -- I have found the probl

Re: [gmx-users] Re: Press Equilibration

On 12/06/2012 9:14 PM, rama david wrote: On Tue, Jun 12, 2012 at 4:40 PM, rama david > wrote: Hi Gromacs Friends, I did NPT for 100 ps with folowing parameter ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen the

Re: [gmx-users] question about pdb file

On 12/06/2012 9:15 PM, delara aghaie wrote: Dear Gromacs users I have encountered in pdb data bank with Human interferon crystal structure: PDB ID : 1ITF http://www.rcsb.org/pdb/explore/explore.do?structureId=1ITF It is mentioned that it contains 24 structures. I opened the file and saw there

Re: [gmx-users] GPU

On 12/06/2012 10:49 PM, Ehud Schreiber wrote: Message: 4 Date: Mon, 11 Jun 2012 15:54:39 +1000 From: Mark Abraham Subject: Re: [gmx-users] GPU To: Discussion list for GROMACS users Message-ID:<4fd5881f.3040...@anu.edu.au> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 11/06/2012

Re: [gmx-users] dihedral restraint MD

On 13/06/2012 2:12 AM, Lin Huang wrote: Hello Everyone, I was willing to conduct umbrella sampling on the dihedrals derived from the sidechains of a ion channel. So i tried dihedral restraint to achieve the goal. However I encountered an awkward problem, hope someone can help me with that. The d

Re: [gmx-users] Re: Can Gromacs functions be called by some other codes?

On 13/06/2012 5:58 AM, Tsjerk Wassenaar wrote: Hey Kai, I would still argue that, from your description, the best solution is a (bash) wrapper script, containing the workflow. If you do that properly, it will result in a much more flexible, readable and maintainable solution. If you end up writi

[gmx-users] Re: bond autocorrelation function

>>> >>> Does gmx provide any script to calculate autocorrelation function >>> for a defined bond (not hydrogen bond autocorrelation function,g_hbond) ? >>> >>> Thanks a lot for the information! >> >> >> Assuming that you mean the aucorrelation function (ACF) of the bond >> length fluctuations aroun

[gmx-users] What does the -don switch calculate in g_hbond?

Hi, In g_hbond, there is an output switch -don, which by default gives an output file named donor.xvg. What does this -don switch calculate? For example, my system contains 22 donors (i.e., oxygens) and 22 hydrogens -- in the form of 22 hydroxyl (OH) groups. My system also contains 1024 accepto

Re: [gmx-users] Re: Can Gromacs functions be called by some other codes?

Hey Kai, I would still argue that, from your description, the best solution is a (bash) wrapper script, containing the workflow. If you do that properly, it will result in a much more flexible, readable and maintainable solution. If you end up writing shell calls in C or Python, you have to sit ba

Re: [gmx-users] Re: Can Gromacs functions be called by some other codes?

In your own code, you should have a system call function, which can be used to run any command in your system. Using C as example, you can write source code like this. /***/ system("g_rms -s xx.tpr -f xx.trr -o rmsd.xvg"); read in file rmsd.xvg t

Re: [gmx-users] problems occur during simulation

On 6/12/12 3:30 PM, abhidon89 wrote: an error occurred while running Grompp Atomtype opls_977 not found i have named atom type in the pdb file opls_977 for phosphorus . The atom type should not appear in the .pdb file. If you have added some new atom type to the OPLS force field, you need

[gmx-users] problems occur during simulation

an error occurred while running Grompp Atomtype opls_977 not found i have named atom type in the pdb file opls_977 for phosphorus . Second how can i make a rtp file ad how is it useful if forcefield residues are not found. -- View this message in context: http://gromacs.5086.n6.nabble.com/prob

Re: [gmx-users] Re: bond autocorrelation function

On 6/12/12 3:23 PM, Dr. Vitaly V. G. Chaban wrote: Hello Does gmx provide any script to calculate autocorrelation function for a defined bond (not hydrogen bond autocorrelation function,g_hbond) ? Thanks a lot for the information! Assuming that you mean the aucorrelation function (ACF) of

[gmx-users] Re: Can Gromacs functions be called by some other codes?

Hi, Dawei, We have some other codes. Sometimes, we can not know the range of the physical parameters we need in advance. When we do the simulation, we may find some required properties are not ready, then we need to run some MD simulations to get the values of the properties. Then the simulation c

[gmx-users] Re: bond autocorrelation function

> Hello > > Does gmx provide any script to calculate autocorrelation function > for a defined bond (not hydrogen bond autocorrelation function,g_hbond) ? > > Thanks a lot for the information! Assuming that you mean the aucorrelation function (ACF) of the bond length fluctuations around its equili

Re: [gmx-users] Can Gromacs functions be called by some other codes?

>From your description, why not just write a script to run various Gromacs programs (MD, analysis, etc)? dawei On Tue, Jun 12, 2012 at 2:43 PM, Bao Kai wrote: > Hi, all, > > I am wondering if Gromacs functions can be called by some other codes. >  I know we get some library files and header file

[gmx-users] Can Gromacs functions be called by some other codes?

Hi, all, I am wondering if Gromacs functions can be called by some other codes. I know we get some library files and header files and we can write our own analysis tools. But I still wonder to what extent the gromacs can be coupled to other codes. For example, can we just generate the topology

[gmx-users] user specified non bonded potentials - regd

Dear Gromacs users, I am planning to use tabulated potentials for the non-bonded interactions for my system. As my system contain some non-bonded interactions in the standard buckingham format and some interactions are similar to buckingham ( i.e., buckingham

Re: [gmx-users] RE: Energy Minimization - not getting correct lipid area

On 6/12/12 12:09 PM, Erica Hicks wrote: Hi, I am still working on this error but found that a possible error could be the way editconf was used to convert .pdb to .gro in Step 3. I used the command: editconf -f dppc128.pdb -o dppc128.gro Is this correct? Would it have been better to use pdb

[gmx-users] dihedral restraint MD

Hello Everyone, I was willing to conduct umbrella sampling on the dihedrals derived from the sidechains of a ion channel. So i tried dihedral restraint to achieve the goal. However I encountered an awkward problem, hope someone can help me with that. The dihedrals of the initial conformation I use

[gmx-users] RE: Energy Minimization - not getting correct lipid area

Hi, I am still working on this error but found that a possible error could be the way editconf was used to convert .pdb to .gro in Step 3. I used the command: editconf -f dppc128.pdb -o dppc128.gro Is this correct? Would it have been better to use pdb2gmx, instead? ( pdb2gmx –f input.pdb –o ou

[gmx-users] bond autocorrelation function

Hello Does gmx provide any script to calculate autocorrelation function for a defined bond (not hydrogen bond autocorrelation function,g_hbond) ? Thanks a lot for the information! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

[gmx-users] Re: Positive Potential Energy after equilibration

Dear Sir, Thank you once again for your reply. I ran the simulation longer. The potential energy has stabilized to around 9000 and does not show a decreasing trend. Also the max hydrogen bond distance is around 0.3 nm. The density of the solid is 1120 kg/m3, couldn't get the density data after its

Re: [gmx-users] Hbonds and PBC

Thank you! I will find out! On Tue, Jun 12, 2012 at 3:41 PM, Justin A. Lemkul wrote: > > > On 6/12/12 10:39 AM, Steven Neumann wrote: > >> Dear Gmx Users, >> >> Do I have to get rid of pbc from my trajectory in order to calculate >> number of >> hydrogen bonds using g_hbond? I mean: Does pbc has

[gmx-users] Re: Hbonds and PBC

My system is made of one ligand and the protein. On Tue, Jun 12, 2012 at 3:39 PM, Steven Neumann wrote: > Dear Gmx Users, > > Do I have to get rid of pbc from my trajectory in order to calculate > number of hydrogen bonds using g_hbond? I mean: Does pbc has any influence > on the number of hydrog

Re: [gmx-users] Hbonds and PBC

On 6/12/12 10:39 AM, Steven Neumann wrote: Dear Gmx Users, Do I have to get rid of pbc from my trajectory in order to calculate number of hydrogen bonds using g_hbond? I mean: Does pbc has any influence on the number of hydrogen bonds? Nearly all Gromacs analysis tools deal with periodicity

[gmx-users] Hbonds and PBC

Dear Gmx Users, Do I have to get rid of pbc from my trajectory in order to calculate number of hydrogen bonds using g_hbond? I mean: Does pbc has any influence on the number of hydrogen bonds? Thank you Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/l

Re: [gmx-users] mdrun_mpi segmentation fault for run in vacuum

On 6/12/12 10:09 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: On 6/12/12 8:48 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: On 6/12/12 7:46 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: On 6/12/12 7:34 AM, reising...@rostlab.informatik.tu-muenchen.de wrote

Re: [gmx-users] mdrun_mpi segmentation fault for run in vacuum

> > > On 6/12/12 8:48 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: >>> >>> >>> On 6/12/12 7:46 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: > > > On 6/12/12 7:34 AM, reising...@rostlab.informatik.tu-muenchen.de > wrote: >>> >>> >>> On 6/12/12 7:05 A

Re: [gmx-users] simulated annealing mdp

Thank you for reply -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface

Re: [gmx-users] simulated annealing mdp

On 6/12/12 9:09 AM, rama david wrote: Hello Justin and Ravi, Lets explain me Why I did simulated anealing?? .. I synthesise peptide and I have experimental data for its self assembly, I just want to reproduced these data. I arranged the 32 protein in axis to petide fibre, in antiparrallel

Re: [gmx-users] simulated annealing mdp

Hello Justin and Ravi, Lets explain me Why I did simulated anealing?? .. I synthesise peptide and I have experimental data for its self assembly, I just want to reproduced these data. I arranged the 32 protein in axis to petide fibre, in antiparrallel Beta sheet structure. I dont have crystal

Re: [gmx-users] mdrun_mpi segmentation fault for run in vacuum

On 6/12/12 8:48 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: On 6/12/12 7:46 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: On 6/12/12 7:34 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: On 6/12/12 7:05 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:

Re: [gmx-users] GPU

>Message: 4 >Date: Mon, 11 Jun 2012 15:54:39 +1000 >From: Mark Abraham >Subject: Re: [gmx-users] GPU >To: Discussion list for GROMACS users >Message-ID: <4fd5881f.3040...@anu.edu.au> >Content-Type: text/plain; charset=ISO-8859-1; format=flowed > >On 11/06/2012 2:32 AM, ifat shub wrote: >> Hi, >>

Re: [gmx-users] mdrun_mpi segmentation fault for run in vacuum

> > > On 6/12/12 7:46 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: >>> >>> >>> On 6/12/12 7:34 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: > > > On 6/12/12 7:05 AM, reising...@rostlab.informatik.tu-muenchen.de > wrote: >>> >>> >>> On 6/12/12 5:54 A

Re: [gmx-users] Re: Positive Potential Energy after equilibration

On 6/12/12 8:26 AM, Satish Kamath wrote: Dear Sir, Thank you for your reply. I just ran NPT and the potential stabilizes at around +9000. The charge distribution change has reduced a lot of potential but it is still positive. My NPT ran for 1ns. Then either the topology is still not suitabl

Re: [gmx-users] simulated annealing mdp

On 6/12/12 8:20 AM, Lord RaviRaj .. wrote: On Tue, Jun 12, 2012 at 4:42 PM, rama david mailto:ramadavidgr...@gmail.com>> wrote: THANK YOU Justin, -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-use

[gmx-users] Re: Positive Potential Energy after equilibration

Dear Sir, Thank you for your reply. I just ran NPT and the potential stabilizes at around +9000. The charge distribution change has reduced a lot of potential but it is still positive. My NPT ran for 1ns. Satish Kamath IISc Bangalore -- View this message in context: http://gromacs.5086.n6.nabb

Re: [gmx-users] simulated annealing mdp

On Tue, Jun 12, 2012 at 4:42 PM, rama david wrote: > THANK YOU Justin, > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don'

Re: [gmx-users] pdb2gmx error

check your aminoacid.rtp file present in /usr/share/gromacs/top/oplsaa.ff/ check all the atom types of that particular residue in your pdb file and match them properly with the atoms types present in the aminoacid.rtp file .and then proceed On Tue, Jun 12, 2012 at 5:29 PM, delara aghaie

Re: [gmx-users] pdb2gmx error

On 6/12/12 7:59 AM, delara aghaie wrote: Dear Gromacs users Using bdp2gmx command to obtain topology and .gro file for 1AU1.pdb I get the following error: I should mention that I have selected OPLS force field. 1) how can I reach to the conclusion that special forcefield is better fo my syste

[gmx-users] pdb2gmx error

Dear Gromacs users Using bdp2gmx command to obtain topology and .gro file for 1AU1.pdb I get the following error: I should mention that I have selected OPLS force field. 1) how can I reach to the conclusion that special forcefield is better fo my system? 2) This is the error: -

Re: [gmx-users] mdrun_mpi segmentation fault for run in vacuum

On 6/12/12 7:46 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: On 6/12/12 7:34 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: On 6/12/12 7:05 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: On 6/12/12 5:54 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:

Re: [gmx-users] mdrun_mpi segmentation fault for run in vacuum

> > > On 6/12/12 7:34 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: >>> >>> >>> On 6/12/12 7:05 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: > > > On 6/12/12 5:54 AM, reising...@rostlab.informatik.tu-muenchen.de > wrote: >> Hi everybody, >> I tried to ru

Re: [gmx-users] mdrun_mpi segmentation fault for run in vacuum

On 6/12/12 7:34 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: On 6/12/12 7:05 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: On 6/12/12 5:54 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I tried to run a minimization just of the hydrogen of a mem

Re: [gmx-users] g_rdf (lyzozyme tutorial)

On 6/12/12 7:24 AM, delara aghaie wrote: Dear Justin I use gromacs (4.0.5). This is the command line: g_rdf -f md_0_1.xtc -s md_0_1.tpr -xy -o rdf.xvg This is what appears on the screen and stops there without any change !!! -

Re: [gmx-users] mdrun_mpi segmentation fault for run in vacuum

> > > On 6/12/12 7:05 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: >>> >>> >>> On 6/12/12 5:54 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I tried to run a minimization just of the hydrogen of a membrane protein. I want to do this in vacuum.

Re: [gmx-users] g_rdf (lyzozyme tutorial)

Dear Justin I use gromacs (4.0.5). This is the command line: g_rdf -f md_0_1.xtc -s md_0_1.tpr -xy -o rdf.xvg This is what appears on the screen and stops there without any change !!! -

[gmx-users] question about pdb file

Dear Gromacs users I have encountered in pdb data bank with Human interferon crystal structure: PDB ID : 1ITF http://www.rcsb.org/pdb/explore/explore.do?structureId=1ITF It is mentioned that it contains 24 structures. I opened the file and saw there are 24 models there. Now if I want to do some

Re: [gmx-users] Press Equilibration

thank you for Quick reply -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www inte

Re: [gmx-users] g_rdf (lyzozyme tutorial)

On 6/12/12 5:16 AM, delara aghaie wrote: Dear Gromacs users Today I encountered a new error. I want to calculte RDF for my protein's (alpha-c) dissolved in water. when I use the command line: g_rdf -f traj.xtc -s topol.tpr -o rdf.xvg and I choose 3 for (C-alpha) for both the reference and tar

[gmx-users] Re: Press Equilibration

On Tue, Jun 12, 2012 at 4:40 PM, rama david wrote: > > Hi Gromacs Friends, > > I did NPT for 100 ps with folowing parameter > > ; Temperature coupling is on > tcoupl= V-rescale; modified Berendsen thermostat > tc-grps= Protein Non-Protein; two coupling groups - more > accur

Re: [gmx-users] Press Equilibration

On 6/12/12 7:10 AM, rama david wrote: Hi Gromacs Friends, I did NPT for 100 ps with folowing parameter ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= Protein Non-Protein; two coupling groups - more accurate tau_t= 0.1

Re: [gmx-users] simulated annealing mdp

THANK YOU Justin, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or

Re: [gmx-users] mdrun_mpi segmentation fault for run in vacuum

On 6/12/12 7:05 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: On 6/12/12 5:54 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I tried to run a minimization just of the hydrogen of a membrane protein. I want to do this in vacuum. But when I started the run wit

[gmx-users] Press Equilibration

Hi Gromacs Friends, I did NPT for 100 ps with folowing parameter ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= Protein Non-Protein; two coupling groups - more accurate tau_t= 0.10.1; time constant, in ps ref_t

[gmx-users] Re: energy conservation: shift vs shifted user potential

Ok, that didn't help me much. Of course I changed both, potential and force to shifted ones. And sure I used a little fortran code to generate the tables -- I have found the problem: I thought GROMACS would ignore the table values above the cutoff distance, but it does not. I added zeros and now i

Re: [gmx-users] mdrun_mpi segmentation fault for run in vacuum

> > > On 6/12/12 5:54 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: >> Hi everybody, >> I tried to run a minimization just of the hydrogen of a membrane >> protein. >> I want to do this in vacuum. >> >> But when I started the run with >> >> mpirun mdrun_mpi -deffnm protein -v -nt 2 >> >>

Re: [gmx-users] mdrun_mpi segmentation fault for run in vacuum

On 6/12/12 5:54 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I tried to run a minimization just of the hydrogen of a membrane protein. I want to do this in vacuum. But when I started the run with mpirun mdrun_mpi -deffnm protein -v -nt 2 I get the error that there is

Re: [gmx-users] Re: Positive Potential Energy after equilibration

On 6/12/12 4:13 AM, Satish Kamath wrote: I've refined the charge distribution. nr type resnr resid atom cgnr charge- prodrg (NEW) mass 1OA 1 F09 OAD 1 -0.117 (-0.596)15.9994 2 H 1 F09 HAD 10.027 (+0.469

Re: [gmx-users] simulated annealing mdp

On 6/12/12 3:39 AM, rama david wrote: Hi Gromacs Friends, I planed to do simulated annealing... My protocol is as follow ( forcefield G96 53a6 spc water model) 1. nvt at 310 k for 100 ps 2. Sa (mdp is posted below ) 3. NPT at 310 k for 100 ps Is it right ?? There are two levels of "righ

[gmx-users] mdrun_mpi segmentation fault for run in vacuum

Hi everybody, I tried to run a minimization just of the hydrogen of a membrane protein. I want to do this in vacuum. But when I started the run with mpirun mdrun_mpi -deffnm protein -v -nt 2 I get the error that there is a segmentation fault. But when I only type mpirun mdrun_mpi there is no p

[gmx-users] g_rdf (lyzozyme tutorial)

Dear Gromacs users Today I encountered a new error. I want to calculte RDF for my protein's (alpha-c) dissolved in water. when I use the command line: g_rdf -f traj.xtc -s topol.tpr -o rdf.xvg and I choose 3 for (C-alpha) for both the reference and target groups, every thing goes well and I will

Re: [gmx-users] radius of gyration

Dear Justin many thanks for your helpful explanation. I did all the checks. the problem was related to the modified .xtc file. (the file created by running trjconv command on the original .xtc file). I do not have any idea that why this command created new .xtc file which was written only to for

[gmx-users] Re: Positive Potential Energy after equilibration

I've refined the charge distribution. nr type resnr resid atom cgnr charge- prodrg (NEW)mass 1OA 1 F09 OAD 1 -0.117 (-0.596) 15.9994 2 H 1 F09 HAD 10.027 (+0.469) 1.0080 3 C

Re: [gmx-users] analysing of the long trajectories

Hi James, Large-scale protein dynamics is low-frequency motion, so you don't need a high time resolution. For large-scale dynamics alone, something in the range of 1000-2500 frames should be sufficient, depending on the size of the system. Note that larger systems require more frames, as there wil

[gmx-users] simulated annealing mdp

Hi Gromacs Friends, I planed to do simulated annealing... My protocol is as follow ( forcefield G96 53a6 spc water model) 1. nvt at 310 k for 100 ps 2. Sa (mdp is posted below ) 3. NPT at 310 k for 100 ps Is it right ?? Please suggest me improvements... Sa mdp file title= gromacs de

Re: [gmx-users] analysing of the long trajectories

Mark, Thanks for advise. As I've found in that link the main way to reduce dimension of the output data is the ussage of appropriate nst* params in the mdp file, exclusion of the solvent from output and finally ussing compres trajectories. Could you tell me what are the most suitable size for th

Re: [gmx-users] Bonds and atom-pairs in g_hbond

Hi, The second set is pairs that are within h-bonding distance but that fails to fulfill the angular criteriion. The text output is hence somewhat misleading. Erik 11 jun 2012 kl. 23.30 skrev Andrew DeYoung: > Hi, > > I am analyzing hydrogen bonds using g_hbond. I have selected two > non-o