[gmx-users] Regarding ngmx

*Dear All, After Installing gromacs, ngmx not seems to work and going through the blogs I understood that it because of some X libraries. Could anybody suggest how to install these libraries and make ngmx work. Thank you* *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangal

Re: [gmx-users] Regarding ngmx

Install libx11-dev (in ubuntu) or something similar before you install gromacs. It worked for me. Luís On 30 November 2011 08:55, Ravi Kumar Venkatraman < ravikumarvenkatra...@gmail.com> wrote: > *Dear All, > After Installing gromacs, ngmx not seems to work and going > through the

[gmx-users] Suppress writing step*.pdb files

Hey :) I think I recall there was a way to suppress writing step*.pdb files, but I couldn't find it. Anyone know from the top of his/her head? Otherwise I'll go and check the source... Oh, trust me... I know what I'm doing ;) Even though it's insane... :D Groetjes, Tsjerk -- Tsjerk A. Wassenaa

[gmx-users] modify the gromacs4.5.5 code: using cout

dear teacher, i want to modify the gromacs4.5.5 code ,can i use function "cout" which is introuduce in c++. i add the code #include #include at the head of the md.c but when i make , there is a error " md.c:103:20: error: iostream: No such file or directory" thanks regards, Bo Du Department o

Re: [gmx-users] modify the gromacs4.5.5 code: using cout

Use fprintf(stdout, "…"); Carsten On Nov 30, 2011, at 12:27 PM, 杜波 wrote: > dear teacher, > > i want to modify the gromacs4.5.5 code ,can i use function "cout" which is > introuduce in c++. > > i add the code > #include > #include > at the head of the md.c > > but when i mak

Re: [gmx-users] Suppress writing step*.pdb files

On 30/11/2011 9:56 PM, Tsjerk Wassenaar wrote: Hey :) I think I recall there was a way to suppress writing step*.pdb files, but I couldn't find it. Anyone know from the top of his/her head? Otherwise I'll go and check the source... Oh, trust me... I know what I'm doing ;) Even though it's insane

Re: [gmx-users] Suppress writing step*.pdb files

Mark Abraham wrote: On 30/11/2011 9:56 PM, Tsjerk Wassenaar wrote: Hey :) I think I recall there was a way to suppress writing step*.pdb files, but I couldn't find it. Anyone know from the top of his/her head? Otherwise I'll go and check the source... Oh, trust me... I know what I'm doing ;)

Re: [gmx-users] Suppress writing step*.pdb files

Thanks guys! I see I'm using an outdated manual... Tsjerk On Wed, Nov 30, 2011 at 1:28 PM, Justin A. Lemkul wrote: > > > Mark Abraham wrote: >> >> On 30/11/2011 9:56 PM, Tsjerk Wassenaar wrote: >>> >>> Hey :) >>> >>> I think I recall there was a way to suppress writing step*.pdb files, >>> but I

[gmx-users] Unit of r in radial distribution function

Hello, Please let me know what is the unit of r (nm or A) in the radial distribution function output(rdf.xvg) of the program g_rdf in gromacs. As the output shows no units. -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.or

Re: [gmx-users] Unit of r in radial distribution function

bipin singh wrote: Hello, Please let me know what is the unit of r (nm or A) in the radial distribution function output(rdf.xvg) of the program g_rdf in gromacs. As the output shows no units. Units used by all programs are discussed in Chapter 2 of the manual. -Justin -- =

Re: [gmx-users] Unit of r in radial distribution function

Hi Bipin, Gromacs uses nm. Cheers, Tsjerk On Wed, Nov 30, 2011 at 3:32 PM, bipin singh wrote: > Hello, > > Please let me know what is the unit of r (nm or A) in the radial > distribution function > output(rdf.xvg) of the program g_rdf in gromacs. As the output shows no units. > > -- >

[gmx-users] g_select

Dear Prof. I have a system consists of 10 micelle after production simulation. How can I select a micelle with 92 monomer? I know that I should use from g_select, but I don't know which argument is proper for me. I also checked -select help in g_select program. Please help me. Best Regards --

Re: [gmx-users] g_select

mohammad agha wrote: Dear Prof. I have a system consists of 10 micelle after production simulation. How can I select a micelle with 92 monomer? I know that I should use from g_select, but I don't know which argument is proper for me. I also checked -select help in g_select program. Please h

Re: [gmx-users] Unit of r in radial distribution function

Thanks. On Wed, Nov 30, 2011 at 20:06, Tsjerk Wassenaar wrote: > Hi Bipin, > > Gromacs uses nm. > > Cheers, > > Tsjerk > > On Wed, Nov 30, 2011 at 3:32 PM, bipin singh wrote: >> Hello, >> >> Please let me know what is the unit of r (nm or A) in the radial >> distribution function >> output(rdf.xv

[gmx-users] how to understand this sentence

The Y-size of the box (1.999239) times the triclinic skew factor (1.00) is smaller than the number of DD cells (2) times the smallest allowed cell size (1.00) I don't understand the fatal error message it has been given during a simple run, I tested with large box already, during editconf

[gmx-users] Re: how to understand this sentence

https://docs.google.com/open?id=0B93SVRfpVVg3NTVjMmY0NzEtM2UzOC00MDEwLWI2OWMtZjEyZDQ5NzM1YWVh I uploaded the files here. is it the box still small? Thanks, On Thu, Dec 1, 2011 at 12:25 AM, lina wrote: > The Y-size of the box (1.999239) times the triclinic skew factor > (1.00) is smaller th

[gmx-users] Hydrophobic cores

Dear Experts, Hi, Is there any tools in gromacs to get "Hydrophobic cores" of protein ? Best, Hyun -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.

[gmx-users] Spherical Position Restrain from the center of the Box

Hello dear GMX Users, Through scripting, I have an itp-like file to restrain all atoms that are NOT within a 30 angstroms radius from the center (a trimmer + water + ions). This selection includes both protein and solvent atoms, which may be a problem when assigning this selection to the TOP fil

Re: [gmx-users] Spherical Position Restrain from the center of the Box

Hi Ricardo, Unfortunately that is not possible. What you can do is rearrange the water in the structure and use two water moleculetypes, one with and one without position restraints. It might be nice to have something like global_position_restraints, added under [ system ], but that needs to be im

Re: [gmx-users] Hydrophobic cores

김현식 wrote: Dear Experts, Hi, Is there any tools in gromacs to get "Hydrophobic cores" of protein ? I suppose that depends on what your definition is, but in all likelihood no, not directly. A program like g_sas can give you nonpolar and polar surface areas as well as volumes and su

[gmx-users] MM/PBSA Gromacs

Dear Gromacs users Is there any script that does a PB or GB calculation to perform a MM/PB(GB)SA free energy calculation in Gromacs. Similar to the MMPBSA.py script available in Amber. I find a similar question raised by a user a couple of years back. Any successful implementation Vijaya

Re: [gmx-users] MM/PBSA Gromacs

Hi! There is support in gromacs for gb calculations. However, I'm currently investigating some recent reports about unstable simulations (unfolding proteins), so my advice is to use the code with caution. Thanks /Per 30 nov 2011 kl. 20:04 skrev "R.S.K.Vijayan" : > Dear Gromacs users > > Is

[gmx-users] gas-phase protein simulation

Hi, I would like to run a gas-phase protein simulation (with charge state of +8). I have read this paper : Biochemistry, 2007, 47, 933-945. In the method section of vaccum simulation, it is said "For the remaining parameters, the same settings were used as in the water simulations, except that

Re: [gmx-users] g_select

mohammad agha wrote: Thanks for your reply, but how can I define residue numbers of one micelle from between 10 micelle that all of them are same and only were differ at the number of monomer in micelle. May I know how, please? Well, now the problem is potentially more complicated. Two app

Re: [gmx-users] gas-phase protein simulation

yes all cutoffs 0 and epsilon_rf 1 and nstlist 0 as well. Toodle pip! On Nov 30, 2011, at 8:39 PM, "Shi, Huilin" wrote: > Hi, > > I would like to run a gas-phase protein simulation (with charge state of > +8). > I have read this paper : Biochemistry, 2007, 47, 933-945. > > In the method se

Re: [gmx-users] gas-phase protein simulation

Shi, Huilin wrote: Hi, I would like to run a gas-phase protein simulation (with charge state of +8). I have read this paper : Biochemistry, 2007, 47, 933-945. In the method section of vaccum simulation, it is said "For the remaining parameters, the same settings were used as in the water

Re: [gmx-users] g_select

Thanks for your reply. Best Regards From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Wednesday, November 30, 2011 11:27 PM Subject: Re: [gmx-users] g_select mohammad agha wrote: > Thanks for your reply, but how can I define residue numbe

[gmx-users] compiling with the PGI compiler

I am using a new cluster of Xeons and, to get the most efficient compilation, I have compiled gromacs-4.5.4 separately with the intel, pathscale, and pgi compilers. With the pgi compiler, I am most concerned about this floating point overflow warning: ... [ 19%] Building C object src/gmxlib/

[gmx-users] compiling with the pathscale compiler hangs on gmx_rms.c.o

Dear users: My compilation with the pathscale compiler hangs for over an hour on the gmx_rms.c.o file (or perhaps the one that comes next). [ 83%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_principal.c.o [ 84%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_polystat.c.o [ 84%

[gmx-users] what's the parameters for angle restraints in mdp file

Dear gmx users: Do anybody know what is the parameters for angle restraints in mdp file, like distance restraint it will have like disre = simple and dihedral restraints will have dihre = yes, and what about for angle restraints? nothing? just defined the force constant and that atom index in t

RE: [gmx-users] gas-phase protein simulation

Hi, Thank you for your reply. My concern is that if rcoulomb and rvdw are set to be zero, does it mean that there are no coulombic and van der waals forces involved in the simulation? I guess there are still coulombic and van der waals forces between atoms of a single protein molecule. Or doe

Re: [gmx-users] gas-phase protein simulation

Shi, Huilin wrote: Hi, Thank you for your reply. My concern is that if rcoulomb and rvdw are set to be zero, does it mean that there are no coulombic and van der waals forces involved in the simulation? I guess there are still coulombic and van der waals forces between atoms of a single

[gmx-users] g_select dynamic indices

Hi Gmxers, I used g_dist to find all water molecules within 5 Angstrom of a protein in a trajectory with a little surprise that gromacs directly prints out those water on my screen rather than in an output file. Since in each frame, those water molecules are not the same, I realize I need to ma

RE: [gmx-users] how to understand this sentence

Have you run g_energy on the .edr file and extracted the box dimensions during the run to see what has been happening to them? Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dalla

[gmx-users] free energy calculation " State B has non-zero total charge: 5.800000e+01 "

Dear gmx users: I am using the free energy to calculate the ligand binding affinity to protein, during the decouple process, I need to put some restraint between the protein and the ligand, e.g. distance restraint. But distance restraint is only for intramolecular, so I need to make a hybrid

Re: [gmx-users] g_select dynamic indices

Yao Yao wrote: Hi Gmxers, I used g_dist to find all water molecules within 5 Angstrom of a protein in a trajectory with a little surprise that gromacs directly prints out those water on my screen rather than in an output file. According to g_dist -h, that's what you should expect :) Since

Re: [gmx-users] free energy calculation " State B has non-zero total charge: 5.800000e+01 "

Chunxia Gao wrote: Dear gmx users: I am using the free energy to calculate the ligand binding affinity to protein, during the decouple process, I need to put some restraint between the protein and the ligand, e.g. distance restraint. But distance restraint is only for intramolecular, so I

[gmx-users] control Distance between the solute and the box for 3 directions seperately

Dear gmx-users, I want to make a long nano-fiber composed of many non-covalently bonded proteins, it elongates along the Z axial direction. in editconf, we can define the "Distance between the solute and the box", but it works for x,y and z directions at the same time. e.g. my command editconf -

Re: [gmx-users] control Distance between the solute and the box for 3 directions seperately

On 1/12/2011 10:24 AM, mu xiaojia wrote: Dear gmx-users, I want to make a long nano-fiber composed of many non-covalently bonded proteins, it elongates along the Z axial direction. in editconf, we can define the "Distance between the solute and the box", but it works for x,y and z directions

Re: [gmx-users] how to understand this sentence

On 1/12/2011 3:25 AM, lina wrote: The Y-size of the box (1.999239) times the triclinic skew factor (1.00) is smaller than the number of DD cells (2) times the smallest allowed cell size (1.00) I don't understand the fatal error message it has been given during a simple run, I tested wit

Re: [gmx-users] control Distance between the solute and the box for 3 directions seperately

mu xiaojia wrote: Dear gmx-users, I want to make a long nano-fiber composed of many non-covalently bonded proteins, it elongates along the Z axial direction. in editconf, we can define the "Distance between the solute and the box", but it works for x,y and z directions at the same time.

[gmx-users] g_select dynamic indices

Hi Justin, Thanks for your hints. I feel the string in g_select is pretty much like tck/tl in VMD. However I have not figured out the way to select a customized group defined in .ndx file. And one more question I have, maybe more general, if I have, say, 100 frames, g_select will give me 1

Re: [gmx-users] g_select dynamic indices

Yao Yao wrote: Hi Justin, Thanks for your hints. I feel the string in g_select is pretty much like tck/tl in VMD. However I have not figured out the way to select a customized group defined in .ndx file. There's one example in the help text that is almost exactly what you want, is it n

Re: [gmx-users] how to understand this sentence

On Thu, Dec 1, 2011 at 7:45 AM, Mark Abraham wrote: > On 1/12/2011 3:25 AM, lina wrote: >> >> The Y-size of the box (1.999239) times the triclinic skew factor >> (1.00) is smaller than the number of DD cells (2) times the >> smallest allowed cell size (1.00) >> >> I don't understand the fa

Re: [gmx-users] how to understand this sentence

Now I used mdrun -nt 2 it showed: Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. and mdrun -nt 1 it showed: Program mdrun, VERSION 4.5.4-dev-20110711-dadcb Source code file: /var/local/cache/

[gmx-users] Analysis of Protein Complex

Dear Sir, I am studying a protein complex. I have perforemed 10ns simulations. I saved snapshots every10ps. sp all snap shopts I got were 1000. Now I want to analyse them with respect to interactions. I want to check the binding surfaces and binding points which come closer and incontact during s

Re: [gmx-users] Analysis of Protein Complex

Hi Saba, You can use g_mdmat or run g_rmsdist for different time windows. It's also a good idea to have a look at all the analysis tools and think of how they may suit your purpose. Cheers, Tsjerk On Thu, Dec 1, 2011 at 5:43 AM, Saba Ferdous wrote: > Dear Sir, > I am studying a protein complex

[gmx-users] Partial atomic charge

Dear GMX users, I could make topology file of a ligand molecule by PRODRG but it has wrong charge on each atom and as mentioned in Gromacs tutorial (protein-ligand complex) I have used quantum mechanic calculation (like spartan) to correct its charge: .itp file from PRODRG: [ atoms ] ; nr

[gmx-users] Re: Looking for potential phosphate binding sites

Hi, Hi, I have done a simulation of 10ns with my proteins and 0.5 M phosphate ion. Now I want to know where does the phosphate ion bind on the protein surface or distribution of phosphate ions on protein surface ?? .. can help me finding out this Regards -- Bharat -- gmx-users mailing li