Re: [gmx-users] Need protein-ligand free energy calculation tutorial

2013-09-19 Thread Sergey Filkin
Actually, http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/ there are two different manuals - one about free energy calculation and other about protein ligand complexes. This page is also can be helpfull http://www.alchemistry.org/wiki/Category:Free_Energy_How-to%27s 2013/9

[gmx-users] Re: Need protein-ligand free energy calculation tutorial

2013-09-19 Thread hsp85
Actually, http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/ there are two different manuals - one about free energy calculation and other about protein ligand complexes. This page is also can be helpfull http://www.alchemistry.org/wiki/Category:Free_Energy_How-to%27s Sergey

Re: [gmx-users] performance issue with the parallel implementation of gromacs

2013-09-19 Thread Carsten Kutzner
Hi, make a scaling test and run on a single node only at first. So you can estimate what performance you can at most expect when going to more nodes. On a single node, you can also run with Gromacs' thread-MPI, thus eliminating the possibility that something with your MPI is wrong. There are lo

[gmx-users] control atom in .hdb file

2013-09-19 Thread xiao
Dear all, I am developing the force field paramters of an organic molecule. I have a trouble when i wrote the hydrogen atom database (.hdb) file. I do not know how to write to control atom. The manual said that: Three or four control atoms (i,j,k,l), where the first always is the atom to whic

Re: [gmx-users] modify nsteps in an existing tpr file

2013-09-19 Thread Mark Abraham
Indeed - your question was fair, and no undue criticism pertained! :-) If you are trying to reproduce something, you must expect .tpr differences between 4.0.x and 4.6.y. I illustrated the change that has taken place in how VDW parameters are used internally in 4.6, and how that is distinct from th

Re: [gmx-users] Selecting certain types of atoms from trajectory file with C++ code

2013-09-19 Thread Justin Lemkul
On 9/19/13 12:33 AM, Zhikun wrote: Dear users, Recently I have been trying to use "xdrfile" libray to read trajectory ".trr" file in my own C++ code. Now I can just read the coordinates of all atoms at each time frame. But I don't know how to select certain types of atoms from the trajectory

Re: [gmx-users] control atom in .hdb file

2013-09-19 Thread Justin Lemkul
On 9/19/13 5:40 AM, xiao wrote: Dear all, I am developing the force field paramters of an organic molecule. I have a trouble when i wrote the hydrogen atom database (.hdb) file. I do not know how to write to control atom. The manual said that: Three or four control atoms (i,j,k,l), where th

Re: [gmx-users] Re: Need protein-ligand free energy calculation tutorial

2013-09-19 Thread Michael Shirts
There are some starter files here: http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_free_energy_calculations%3a_Michael_Shirts%2c_Session_2A Which can be used in conjunction with the Alchemistry.org instructions. But it needs to be update

[gmx-users] MPI runs on a local computer

2013-09-19 Thread Xu, Jianqing
Dear all, I am learning the parallelization issues from the instructions on Gromacs website. I guess I got a rough understanding of MPI, thread-MPI, OpenMP. But I hope to get some advice about a correct way to run jobs. Say I have a local desktop having 16 cores. If I just want to run jobs on

Re: [gmx-users] performance issue with the parallel implementation of gromacs

2013-09-19 Thread ashutosh srivastava
Thank you Carsten Will surely try out the suggestions and get back to you On Thu, Sep 19, 2013 at 1:52 PM, Carsten Kutzner wrote: > Hi, > > make a scaling test and run on a single node only at first. So you can > estimate what performance you can at most expect when going to more nodes. > > On

Re: [gmx-users] protein unfolding in water

2013-09-19 Thread Justin Lemkul
On 9/19/13 10:12 AM, fatemeh ramezani wrote: dear users I'm studying gold nano-particle effect on one of the blood protein stability and structure. one time I simulated the protein in the presence of the gold nanoparticle and once without nanoparticles. when I simulated protein alone in wa

Re: [gmx-users] Problem with http://www.gromacs.org/Documentation/Tutorials page

2013-09-19 Thread Justin Lemkul
On 9/19/13 10:38 AM, Ray Sheppard wrote: Hello, On the page sited above, it says: General GROMACS Use * A step-by-step demo and several simple examples are available in the share/tutor subdirectory of your GROMACS installation. However, In the tarfile for version 4.6.3, the

[gmx-users] Problem with http://www.gromacs.org/Documentation/Tutorials page

2013-09-19 Thread Ray Sheppard
Hello, On the page sited above, it says: General GROMACS Use * A step-by-step demo and several simple examples are available in the share/tutor subdirectory of your GROMACS installation. However, In the tarfile for version 4.6.3, the directories under "share" are: rsheppar@login

Re: [gmx-users] modify nsteps in an existing tpr file

2013-09-19 Thread Guanglei Cui
Thanks, Mark. Just compiled gmx 4.0.5 and created tpr with the 'published' topology file. Ver. 4.0.5 seems to be the version that was used to create the 'published' tpr file. The only differences now that matter are these c6 and c12 terms. Is there any mdp options that may change how c6 and c12 a

[gmx-users] protein unfolding in water

2013-09-19 Thread fatemeh ramezani
dear users I'm studying gold nano-particle effect on one of the blood protein stability and structure. one time I simulated the protein in the presence of  the gold nanoparticle and once without nanoparticles. when I simulated protein alone in water, I expected the protein to remain stable but

Re: [gmx-users] Re: grompp for minimization: note & warning

2013-09-19 Thread Tsjerk Wassenaar
Hi Shahab, You edited the .gro file, but you made an error. So you have to read the manual to understand the file format and then see where and how your edited file doesn't match. Cheers, Tsjerk On Thu, Sep 19, 2013 at 5:00 PM, shahab shariati wrote: > Dear Tsjerk > > Thanks for your consider

[gmx-users] Re: grompp for minimization: note & warning

2013-09-19 Thread shahab shariati
Dear Tsjerk Thanks for your consideration. I ignored Warning 1. > WARNING 1 [file topol.top, line 32]: > 3632 non-matching atom names > atom names from topol.top will be used > atom names from system.gro will be ignored Based on your suggestion, I checked non-matching atom names between t

Re: [gmx-users] Regarding g_sgangle index file

2013-09-19 Thread Venkat Reddy
Dear Sir, The tool "gmx gangle" is wonderful. The additional options are very flexible and easy to use. @Teemu Murtola: Are there any modifications to the other gmx tools? (eg: rdf calculation with dynamic selection...etc). I am trying to explore the new version. Thank you On Tue, Sep 17, 2013 a

Re: [gmx-users] forcefield and setting

2013-09-19 Thread Justin Lemkul
On 9/19/13 11:59 AM, fatemeh ramezani wrote: Dear Justin I used gromacs OPLSAA forcefield for simulation of protein and TIP3P model for water. em.mdp file: title = n.pdb cpp = /lib/cpp define = -DFLEXIBLE constraints = none integrator

[gmx-users] Charmm 36 forcefield with verlet cut-off scheme

2013-09-19 Thread akk5r
Hey All, I am running a simulation of a POPC bilayer in water using a Charmm 36 forcefield. I am having trouble using cutoff-scheme=Verlet in my nvt equilibration. My .mdp file is as follows: title= OPLS Lysozyme NVT equilibration define = -DPOSRES ; position restrain the protein

[gmx-users] forcefield and setting

2013-09-19 Thread fatemeh ramezani
 Dear Justin I used gromacs OPLSAA forcefield for simulation of protein and TIP3P model for water. em.mdp file: title   =  n.pdb cpp =  /lib/cpp define  =  -DFLEXIBLE constraints =  none integrator  =  steep nsteps  =  4 co

[gmx-users] SDFs memory allocation error

2013-09-19 Thread Marta Batista
Hi, I am trying to perform SDFs using g_spatial tool from Gromacs. I did all steps, recommended and indicated in Gromacs' manual, 1. Use make_ndx to create a group containing the atoms around which you want the SDF 2. trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none 3. trj

Re: [gmx-users] Charmm 36 forcefield with verlet cut-off scheme

2013-09-19 Thread Justin Lemkul
On 9/19/13 2:21 PM, akk5r wrote: Hey All, I am running a simulation of a POPC bilayer in water using a Charmm 36 forcefield. I am having trouble using cutoff-scheme=Verlet in my nvt equilibration. My .mdp file is as follows: title= OPLS Lysozyme NVT equilibration define = -DPOSRES

Re: [gmx-users] SDFs memory allocation error

2013-09-19 Thread Justin Lemkul
On 9/19/13 2:56 PM, Marta Batista wrote: Hi, I am trying to perform SDFs using g_spatial tool from Gromacs. I did all steps, recommended and indicated in Gromacs' manual, 1. Use make_ndx to create a group containing the atoms around which you want the SDF 2. trjconv -s a.tpr -f a.xtc -o b.x

Re: [gmx-users] changing atom types versus adding dihedrals to atom types

2013-09-19 Thread Rafael I. Silverman y de la Vega
Hmm, I will have to do some more controls then, but I prob dont have time to do them till after quals this fall... You mention Hartree-Fock methods, does this mean that you disfavor DFT for some reason for this purpose? On Tue, Sep 17, 2013 at 5:40 PM, Justin Lemkul wrote: > > > On 9/17/13 8:1

Re: [gmx-users] changing atom types versus adding dihedrals to atom types

2013-09-19 Thread Rafael I. Silverman y de la Vega
Sulpher is important, but it is in the apoprotein, not the parametrized prosthetic group On Thu, Sep 19, 2013 at 6:51 PM, Rafael I. Silverman y de la Vega < rsilv...@ucsc.edu> wrote: > Hmm, I will have to do some more controls then, but I prob dont have time > to do them till after quals this f

[gmx-users] Re: Charmm 36 forcefield with verlet cut-off scheme

2013-09-19 Thread akk5r
Thanks Justin. I was told that the "vdwtype = switch" was an essential component of running Charmm36. Is that not the case? -- View this message in context: http://gromacs.5086.x6.nabble.com/Charmm-36-forcefield-with-verlet-cut-off-scheme-tp5011322p5011328.html Sent from the GROMACS Users Forum m

Re: [gmx-users] changing atom types versus adding dihedrals to atom types

2013-09-19 Thread Justin Lemkul
On 9/19/13 9:51 PM, Rafael I. Silverman y de la Vega wrote: Sulpher is important, but it is in the apoprotein, not the parametrized prosthetic group I only mentioned this as one example where user input and intuition is useful, not necessarily to directly comment on anything you are doing.

Re: [gmx-users] changing atom types versus adding dihedrals to atom types

2013-09-19 Thread Justin Lemkul
On 9/19/13 9:51 PM, Rafael I. Silverman y de la Vega wrote: Hmm, I will have to do some more controls then, but I prob dont have time to do them till after quals this fall... You mention Hartree-Fock methods, does this mean that you disfavor DFT for some reason for this purpose? For CHARMM,

Re: [gmx-users] Re: Charmm 36 forcefield with verlet cut-off scheme

2013-09-19 Thread Justin Lemkul
On 9/19/13 9:55 PM, akk5r wrote: Thanks Justin. I was told that the "vdwtype = switch" was an essential component of running Charmm36. Is that not the case? It is, but I suppose one can achieve a similar effect with the Verlet scheme. You can certainly use the traditional CHARMM settings if

[gmx-users] Fatal Error: Residue 'DMP' not found in residue topology database

2013-09-19 Thread Santhosh Kumar Nagarajan
Hi guys, The error I'm getting is as follows "All occupancies are one Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomtypes.atp Atomtype 1 Reading residue database... (oplsaa) Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.rtp Residu