[gmx-users] Representative structure from MD trajectories

Hello, I have constructed a 2-d FEL using PC1 and PC2 as the reaction coordinates(by using g_sham). >From this 2-d FEL, I extracted the PC1 and PC2 (principal components) values corresponding to minimum free energy. Then I extracted the time during which system possess these PC's values( by lookin

Re: [gmx-users] radial distribution function

lina wrote: On Sat, Sep 10, 2011 at 3:35 AM, Moeed > wrote: Dear users, I have created radial distribution function plot for Carbon atoms in a system containing polymer chains. I see some little jumps between first and second peak. I need

Re: [gmx-users] radial distribution function

On Sat, Sep 10, 2011 at 3:35 AM, Moeed wrote: > Dear users, > > I have created radial distribution function plot for Carbon atoms in a > system containing polymer chains. I see some little jumps between first and > second peak. > I need your help to comment on how this behavior can be justified (

Re: [gmx-users] radial distribution function

Moeed wrote: On Fri, Sep 9, 2011 at 4:18 PM, Justin A. Lemkul > wrote: Moeed wrote: Thank you Justin for your reply. Simulation is 5 ns long ( before this a 500 ps NVT was done as equilibration) and total energy has been equilibrated af

Re: [gmx-users] radial distribution function

On Fri, Sep 9, 2011 at 4:18 PM, Justin A. Lemkul wrote: > > > Moeed wrote: > >> Thank you Justin for your reply. Simulation is 5 ns long ( before this a >> 500 ps NVT was done as equilibration) and total energy has been equilibrated >> after around 3 ns. >> >> -b is set to 4000 that is the last

Re: [gmx-users] dialanine using charmm27 ff

Hi Mark It worked ! pdb2gmx is now properly processing the pdb, and moreover the potential energy from gmx is within 1.27 kJ/mol of that from Charmm. More on energy comparison shortly. However, further tinkering of the rtp and pdb file was required to generate the topology: 1. The original rtp en

Re: [gmx-users] (no subject)

Алексей Раевский wrote: Hi. I've look through the manual and didn't find an answer on my question: i've got a trajectory and i want to convert it in *.pdb with such parameters of index file [all atoms within a sphere with a chosen radius around selected atom]. What can i do? Thank you Use

[gmx-users] (no subject)

Hi. I've look through the manual and didn't find an answer on my question: i've got a trajectory and i want to convert it in *.pdb with such parameters of index file [all atoms within a sphere with a chosen radius around selected atom]. What can i do? Thank you -- *С уважением! *** * Nemo me

Re: [gmx-users] gromacs 4.5 tools for trajectory analysis

Hasan haska wrote: Dear gromacs users, I loaded my .psf and then loaded .pdb file into psf in VMD then used the command “ topo writegmxtop myfile.top” in tk console. I finally generated a gromacs .top file successfully. I want to use gromacs 4.5 tools for trajectory analysis with namd dcd

Re: [gmx-users] radial distribution function

Moeed wrote: Thank you Justin for your reply. Simulation is 5 ns long ( before this a 500 ps NVT was done as equilibration) and total energy has been equilibrated after around 3 ns. -b is set to 4000 that is the last 1 ns has been used for rdf. For all but the simplest systems this simul

[gmx-users] gromacs 4.5 tools for trajectory analysis

Dear gromacs users, I loaded my .psf and then loaded .pdb file into psf  in VMD then used the command “ topo writegmxtop myfile.top” in tk console. I finally generated a gromacs .top file successfully. I want to use gromacs 4.5 tools for trajectory analysis with namd dcd and pdb files. But how

[gmx-users] Help OPLS-AA system explodes

Dear Gromacs Users: I've been working with small unsaturated hydrocarbons using OPLS-AA with NVT calculations using box dimensions according to : x=y & z=3x centered in 1/2x,1/2y,1/2z in order to obtain surface tension. My system expands at the begging of the mdrun calculation until it occupies the

Re: [gmx-users] radial distribution function

Thank you Justin for your reply. Simulation is 5 ns long ( before this a 500 ps NVT was done as equilibration) and total energy has been equilibrated after around 3 ns. -b is set to 4000 that is the last 1 ns has been used for rdf. Best, moeed On Fri, Sep 9, 2011 at 3:37 PM, Justin A. Lemkul w

Re: [gmx-users] radial distribution function

Moeed wrote: Dear users, I have created radial distribution function plot for Carbon atoms in a system containing polymer chains. I see some little jumps between first and second peak. I need your help to comment on how this behavior can be justified (or if the plot is wrong). g_rdf -f *.

[gmx-users] radial distribution function

Dear users, I have created radial distribution function plot for Carbon atoms in a system containing polymer chains. I see some little jumps between first and second peak. I need your help to comment on how this behavior can be justified (or if the plot is wrong). g_rdf -f *.trr -s *.tpr -o *.xvg

Re: [gmx-users] pull code: distance between pull grp and ref grp is more than usual at the begining of simulation (at 1st time frame 1 ps)

Shilpi Chaurasia wrote: I am trying to pull apart two dimers of tubulin protein joined together, to form two separate dimers by steered molecular dynamics using Pull code. The objective is to separate the dimers by pulling along one axis only (Y axis). I ran the simulation for 25 ps and it

[gmx-users] pull code: distance between pull grp and ref grp is more than usual at the begining of simulation (at 1st time frame 1 ps)

 I am trying to pull apart two dimers of tubulin protein joined together, to form two separate dimers by steered molecular dynamics using Pull code. The objective is to separate the dimers by pulling along one axis only (Y axis). I ran the simulation for 25 ps and it accomplished well but while

[gmx-users] Re: amb2gmx.pl to convert GLYCAM topology

x27;t post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.o

Re: [gmx-users] building GROMACS 4.5.4 on Power6 with CMAKE

On 9/09/2011 10:01 PM, Marcin Zielinski wrote: Ok, giving -DGMX_ACCELERATE=Power6 results with: src/config.h /* Define to a macro mangling the given C identifier (in lower and upper case), which must not contain underscores, for linking with Fortran. */ #define F77_FUNC(name,NAME) name

Re: [gmx-users] md.mdp file GPU one

On Fri, Sep 9, 2011 at 8:48 PM, Justin A. Lemkul wrote: > > > lina wrote: > >> Hi, >> >> >> are there someone love to share one md.mdp file for GPU version? >> >> > All the details are here: > > http://www.gromacs.org/**Downloads/Installation_** > Instructions/GPUs?highlight=**gpu

Re: [gmx-users] Density

vferra...@units.it wrote: Dear all, I want to calculate the density of my system and visualize it during the simulation time. I've tried with g_density and with g_energy but in all the cases the density calculated is the average density all along the simulation and not the density of all th

[gmx-users] Density

Dear all, I want to calculate the density of my system and visualize it during the simulation time. I've tried with g_density and with g_energy but in all the cases the density calculated is the average density all along the simulation and not the density of all the system in each step of

Re: [gmx-users] Re: g_sas of ligands

Steven Neumann wrote: Was my question not clear or noone can help me? I am wondering whether calculations of ligand hydrophobic SAS (decrease during the simualtion) can be result of binding to protein? Presumably it's due to both aggregation and binding to the protein, if, in fact both

[gmx-users] Re: g_sas of ligands

Was my question not clear or noone can help me? I am wondering whether calculations of ligand hydrophobic SAS (decrease during the simualtion) can be result of binding to protein? On Fri, Sep 9, 2011 at 8:23 AM, Steven Neumann wrote: > Dear Gromacs Users, > > I am calculating SAS using g_sas of

[gmx-users] atom type OXT

You still haven't provided all of the relevant information. For example: what ff are you using? But please don't just sent that information now... better for you to read about how to develop a good post and next time be suer to include enough information that we could reproduce the problem

Re: [gmx-users] md.mdp file GPU one

lina wrote: Hi, are there someone love to share one md.mdp file for GPU version? All the details are here: http://www.gromacs.org/Downloads/Installation_Instructions/GPUs?highlight=gpu The benchmark archive has example .mdp files that you can tweak. -Justin -- =

[gmx-users] md.mdp file GPU one

Hi, are there someone love to share one md.mdp file for GPU version? Thanks ahead, -- Best Regards, lina -- 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 b

[gmx-users] building GROMACS 4.5.4 on Power6 with CMAKE

Ok, giving -DGMX_ACCELERATE=Power6 results with: src/config.h /* Define to a macro mangling the given C identifier (in lower and upper case), which must not contain underscores, for linking with Fortran. */ #define F77_FUNC(name,NAME) name ## /* As F77_FUNC, but for C identifiers contain

Re: [gmx-users] Groamacs for metal ion

On 09/09/11, om prakash wrote: > > Dear friends > > I am trying to gromacs simulation with the metal (Zn) binding protein. But > here, i am not able to make itp file for the metal..I am preety new to this > field...anyone please suggest me, what i should do? > You should endeavour to

Re: [gmx-users] dialanine using charmm27 ff

On 09/09/11, Sandeep Somani wrote: > Hi Mark > > > Thanks for the rtp definitions. I added the rtp defs to aminoacids.rtp and > renamed residue and atom names in pdb file. > > > But pdb2gmx is still complaining about the terminal groups. It seems to have > picked up ACE, but not CT3.

[gmx-users] Groamacs for metal ion

Dear friends I am trying to gromacs simulation with the metal (Zn) binding protein. But here, i am not able to make itp file for the metal..I am preety new to this field...anyone please suggest me, what i should do? -- Om Prakash Sharma Ph.D Scholar & DIT JRF Centre for Bioinformatics Pondicherr

Re: [gmx-users] dialanine using charmm27 ff

Hi Mark Thanks for the rtp definitions. I added the rtp defs to aminoacids.rtp and renamed residue and atom names in pdb file. But pdb2gmx is still complaining about the terminal groups. It seems to have picked up ACE, but not CT3. pdb2gmx error message and modified pdb file are listed below. Any

Re: [gmx-users] amb2gmx.pl to convert GLYCAM topology

Or why not trying acpype? Cheers, Alan On 9 September 2011 07:37, Mark Abraham wrote: > On 9/09/2011 4:21 PM, Yun Shi wrote: > > Hi all, > > I understand this problem has been discussed before, but it seems no > conclusion has been drawn. > > > Someone needs to do some work and report back :-

Re: [gmx-users] building GROMACS 4.5.4 on Power6 with CMAKE

On 9/09/2011 5:50 PM, Marcin Zielinski wrote: Hi Mark, Yes, GMX_ACCELERATION should do the trick, however it requires You to turn off the THREADS. Altho ppl tend to run the tools in serial anyway, I somehow sticked to that. Only mdrun takes advantage of parallelism in GROMACS up to now. So t

[gmx-users] building GROMACS 4.5.4 on Power6 with CMAKE

Hi Mark, Yes, GMX_ACCELERATION should do the trick, however it requires You to turn off the THREADS. Altho ppl tend to run the tools in serial anyway, I somehow sticked to that. As for the FindLAPACK.cmake fix, I'm pretty sure I has been posted here some time ago. I googled it anyhow. Would

Re: [gmx-users] gridcount

On 9/09/2011 5:27 PM, aiswarya pawar wrote: Hi all, am facing an error while installing gridcount- make[1]: *** [g_ri3Dc.o] Error 1 make[1]: Leaving directory `/home/proj11/aiswarya/Grid-count/src' make: *** [all] Error 2 This error is while giving the make command. This is not the right for

[gmx-users] gridcount

Hi all, am facing an error while installing gridcount- make[1]: *** [g_ri3Dc.o] Error 1 make[1]: Leaving directory `/home/proj11/aiswarya/Grid-count/src' make: *** [all] Error 2 This error is while giving the make command. Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.

[gmx-users] g_sas of ligands

Dear Gromacs Users, I am calculating SAS using g_sas of ligands in my system: protein, 30 ligands in water. The hydrophobic SAS of ligands decrease and reach stable value. Hydrophilic remains stable over the simulation time. I am wondering whether it (the decrease o hydrophobic) is because of bin