Re: [gmx-users] Problem sasa 3.2.1 vs 3.3.2

e in a head belonging to a > developer). > > Cheers, > > Tsjerk > > On Thu, Sep 18, 2008 at 3:39 PM, Anthony Cruz <[EMAIL PROTECTED]> wrote: > > Hi users: > > Recently I run a simulation of a protein in DMSO with GROMACS 3.2.1. I > > make the analysis wi

[gmx-users] chromophore parameters for Molecular Dynamics

Hi users: I am working in a new projec and we plan to do some molecular dynamic experiment to an engineered GFP molecule. I have been searching for the parameters for the GFP chromophore without success. Can some one help me? Any reference or parameters?? Best Regards, Anthony __

[gmx-users] How constraint structure not conformation

Hi User: We have a protein with two domains. This two domains were connected by two linkers of different length. We want to study the different conformation that the protein domains can adopt depending the length of the linkers without loosing the secondary structure feature present. I was think

[gmx-users] Conformation search!

Hi User: We have a protein with two domains. This two domains were connected by two linkers of different length. We want to study the different conformation that the protein domains can adopt depending the length of the linkers without loosing the secondary structure feature present. I was think

Re: [gmx-users] Conformation search!

On Thursday 17 April 2008 9:13 pm, Mark Abraham wrote: > Anthony Cruz wrote: > > Hi User: > > We have a protein with two domains. This two domains were connected by > > two linkers of different length. We want to study the different > > conformation that the protein doma

Re: [gmx-users] Conformation search!

On Friday 18 April 2008 10:37 am, Mark Abraham wrote: > Anthony Cruz wrote: > > > You seem to want to let your domains move relative to each other, but > > > > > > also to deny them much internal freedom. So what you want to do is > > > > > >

[gmx-users] LJ question

Dear Users: I am planing to do some simulations of a protein in acetonitrile using the model of P.J. Gee (Mol. Phys. (2006) 104, 477-483). The use of this model will introduce new atom types and new LJ parameters for those atoms. When I define those atoms in the acetonitrile topology I need to d

Re: [gmx-users] LJ question

Thank you for your rapidly responce David. If I use thr Gromos96 (ff43a1) it will do it? How I check if the force field allows mixing? Cheers, Anthony On Thursday 28 August 2008 01:34:30 pm David van der Spoel wrote: > Anthony Cruz wrote: > > Dear Users: > > I am planing to do s

[gmx-users] Problem sasa 3.2.1 vs 3.3.2

Hi users: Recently I run a simulation of a protein in DMSO with GROMACS 3.2.1. I make the analysis with GROMACS 3.3.2 and GROMACS 3.2.1 . When I do the sasa analysis I observe differences in the sasa values between the two versions. The total sasa seems to be same in the two graphs but the hydr

[gmx-users] Continuation diferent machine.

Hi users: I have made some simulation in one of our workstation. Now I want to extend the simulations few nanoseconds. I can continue the simulations in other machine without affecting the results? I need to use the same gromacs version? Best Regards, Anthony __

Re: [gmx-users] Continuation diferent machine.

hat > depends on the compiler, or if you are running on architectures where > we use tuned assembly loops. > > > Cheers, > > Erik > > On Aug 7, 2007, at 10:57 PM, Anthony Cruz wrote: > > Hi users: > > I have made some simulation in one of our workstation. Now I wan

Re: [gmx-users] Continuation diferent machine.

gt; This is normally only important for debugging. If you don't know it > doesn't apply to you :-) > > All that matters for you is that 3.3 >= 3.2, so it should work fine; > the hardware doesn't matter. > > Cheers, > > Erik > > On Aug 8, 2007, at 12:25

Re: [gmx-users] freeze water

On Friday 28 April 2006 12:02 pm, David van der Spoel wrote: > Anthony Cruz wrote: > > Hi: > > I want to make a simulation of a small pepetide in a box of water but I > > want to freeze or restrain the movement of all water molecules that have > > a distance grate

Re: [gmx-users] freeze water

What procedure will be better? Freeze or position restrain? Anthony On Monday 01 May 2006 7:17 am, Anthony Cruz wrote: > On Friday 28 April 2006 12:02 pm, David van der Spoel wrote: > > Anthony Cruz wrote: > > > Hi: > > > I want to make a simulation of a small pepet

[gmx-users] topology transformation

Hi users: How I can convert a topology generated by PRODRG topology generation server to a gromos topology??? or I cant use it with the G43a1 GROMOS96 43a1 Forcefield thanks Anthony ___ gmx-users mailing listgmx-users@gromacs.org http://www.gro

[gmx-users] Topology question

Hi users: I made a small molecule topology using the PRODRG topology generation server but I want to use it with the G43a1 GROMOS96 43a1 Forcefield. How I could change the parameters from GROMACS to GROMOS??? thanks Anthony ___ gmx-users mailing

[gmx-users] Solventbox equilibration

Hi: I have been trying to made a solvent box of methacrylic acid using parameters from PRODRG. I change it to GROMOS96 parameters and use charges from DFT calculation. I do the energy minimization with out any problem. I run a 2ns MD (NVT) with out any problem too. But when I try to run an MD

[gmx-users] PDB2GMX PROBLEM: *** buffer overflow detected ***: pdb2gmx terminated

Hi: I want to run a simulation of a heme protein. I found that in the gromacs site the bug in the specbond.c and I download this file from bugzilla. I substitute this file in the source and try to build a new rpm to install. When I instal the new rpm and try to use pdb2gmx the progam stop with t

[gmx-users] PDB2GMX PROBLEM: *** buffer overflow detected ***: pdb2gmx terminated

Hi: I want to run a simulation of a heme protein. I found that in the gromacs site the bug in the specbond.c and I download this file from bugzilla. I substitute this file in the source and try to build a new rpm to install. When I instal the new rpm and try to use pdb2gmx the progam stop with t

[gmx-users] Different gromacs version question

Hi: is possible to run a system that I prepared with the 3.2.1 version in the 3.3.1 without problems??? Anthony ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe request

[gmx-users] Heme parameters

Hi: Where I can find parameter for ferric heme??? Best regards Anthony ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or s

[gmx-users] L-J question

Hi users: I have a little question. I found some L-J parameters for heme iron for the GROMOS87 FF and I want to use it in the GROMOS ff43a1 . The units as appear in the paper [biophys. J. 1995 (69) p810] A(kJ nm^ -12 mol ^-1) 4.30115e-5 and B (kJ nm^ -6 mol ^ -1) 8.886909e-3. I need to make any

[gmx-users] gromos87 to gromos96

Hi: How to convert gromos87 ferric iron heme l-j parameters: 4.30115e-5(kJ nm^-12 mol^-1) and 8.86909e-3(kJ nm^-6 mol^-1) to use it in gromos96 FF? Anthony ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-

[gmx-users] Dummy Problem.

Hi Users: I have a question about dummy atoms. I try to simulate a protein that have a cysteine modified with a NO group. I found a NO model that have 3 sites, one at each atom and other in the center of mass (Biophys. Chem. 98 (2002) 183). [ SNC ] [ atoms ] N N-0.28000 0

Re: [gmx-users] Dummy Problem.

collapsing of the dummy atom. What could be the problem??? Anthony On Tuesday 06 February 2007 8:08 pm, Mark Abraham wrote: > Anthony Cruz wrote: > > Hi Users: > > > > > > In my topology before all the bonded information I add the following > > lines with the approp

Re: [gmx-users] parameters for nitric oxide (NO)

Hi Jochen: Did you receive any responce??? I font 2 different parameters for NO. one of 2 sites and other of three sites. I try to build the three sithe model but I can get it to work because I have problems with the third site, a dummy atom. Probably you have more experience with GROMACS than m

[gmx-users] gromacs manual

Hi: I have been trying to make the manual from cvs and I can make it. If someone have it please could send me a copy ??? Thanks Anthony ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't p

[gmx-users] freeze water

Hi: I want to make a simulation of a small pepetide in a box of water but I want to freeze or restrain the movement of all water molecules that have a distance grater that 3 A from the protein surface. Right know the water that are within 3 A of the protein, have a different residue name (SHL)

Re: [gmx-users] Problem with FE-Cys covalent bond

Hi: Did you add the parameters for the new covalent bond to the correct part of ffbonded.itp? Because, for the GROMOS FF you have to add the parameters for the new bond, angle and dihedral ,created due to specbond, in a certain part of the ffbonded.itp for pdb2gmx be able to use it. I dont know if

[gmx-users] tpbconv and tpr file problem...

Hi Users: I was trying to calculate the energy contribution of an specific ion in my simulation. After extract a given frame from the simulation, I recalculate the energies of this frame with mdrun -rerun. Then I used tpbconv and editconf to create a new gro file and a new tpr without the ion. I t

Re: [gmx-users] tpbconv and tpr file problem...

On Wed, Mar 14, 2012 at 8:42 PM, Mark Abraham wrote: > On 15/03/2012 5:33 AM, Anthony Cruz Balberdi wrote: > >> Hi Users: >> >> I was trying to calculate the energy contribution of an specific ion in >> my simulation. After extract a given frame from the simulation,

Re: [gmx-users] tpbconv and tpr file problem...

Thanks On Fri, Mar 16, 2012 at 10:37 AM, Mark Abraham wrote: > On 17/03/2012 12:39 AM, Anthony Cruz Balberdi wrote: > > > On Wed, Mar 14, 2012 at 8:42 PM, Mark Abraham wrote: > >> On 15/03/2012 5:33 AM, Anthony Cruz Balberdi wrote: >> >>> Hi Users: >>

[gmx-users] Tesla M2075 error...

Hi user: I was able to compile gromacs with GPU support without errors, but when I test it with the benchmark got the following error: (mdrun-gpu -device "OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=no" -s topol.tpr -v) Fatal error: The selected GPU (#0, Tesla M2075) is not supported

Re: [gmx-users] Tesla M2075 error...

Thanks! On Tue, Oct 16, 2012 at 10:00 AM, Justin Lemkul wrote: > > > On 10/16/12 9:58 AM, Anthony Cruz Balberdi wrote: > >> Hi user: >> >> I was able to compile gromacs with GPU support without errors, but when I >> test it with the benchmark got the follo

[gmx-users] Gromacs compilation on AMD multicore

Dear Users: We recently received our new computer. This computer have 4 multicore Opteron AMD cpus and I am planning to install GROMAS. Which options I will need to use in order to achieve the best possible performance? Which compiler GNU or Intel? Thank you for all you help. Anthony -- gmx-us

Re: [gmx-users] Gromacs compilation on AMD multicore

than FFTW3, last I tested, but much more fiddly to link. > > Mark > > > On Tue, Jul 5, 2011 at 10:26 AM, Matthew Zwier wrote: >> >>> Hi Anthony, >>> >>> The default options are nearly optimal, and the difference between a >>> modern (4.4

[gmx-users] Gromacs compilation

rn 0; | } configure:4477: error: in `/home/acruz/bin/GROMACS_SUITE/development/gromacs-4.5.4': configure:4481: error: C compiler cannot create executables See `config.log' for more details. How I could solve the problem? Best regards, Anthony Cruz -- gmx-users mailing listgmx-use

[gmx-users] Protein encapsulation

Dear user: I am planning to run some simulations of a protein encapsulated using a rigid polymer but I not sure of what approach will be better. I was thinking in using position restraint or freeze groups. Which procedure will not cause problems or artifacts in the simulation? Any other idea on ho

Re: [gmx-users] Convert trr into crd (amber format)

I think that you can do it in vmd On Tue, Jul 7, 2009 at 11:18 PM, Ragnarok sdf wrote: > I came across a tool for making "porcupine" plots out of my PCA > analysis, but first I need to perform the analysis with a program that > accepts .cdr (amber traj) file format (the name of the program is >

Re: [gmx-users] monomers

Other way to do it is to edit the spectbond.dat for serach the atoms that you want to bond. The same way that gromacs made the bond between the HEME and the HIS On Mon, Jul 13, 2009 at 6:27 PM, Jarol E. Molina wrote: > Hi all > > I need some monomers get bonds among them, but each one does not ha

[gmx-users] Salt concentration

Dear Users: I am interested in perform a simulation of a protein in different salt concentrations. How I can calculate how much Na+ and Cl- ions to include in the simulation to achieve certain concentration? Could someone point me in the right direction? Is there a software to do this type of calcu

Re: [gmx-users] Salt concentration

Thank you Gonçalo and Dallas for your help. Best Regards Anthony 2010/9/27 Gonçalo C. Justino : > Hi Anthony, > You can use the '-conc' tag from genion during file preparation, as > per http://manual.gromacs.org/current/online/genion.html. > Gonçalo > > On 27 Septem

Re: [gmx-users] Parameterization

Dear Yuvraj: There is a protocol to find the charges and force field parameters for new molecules for the AMBER force field. The best way is to try to find the parameters from a publication. If you dont find anything then use RED to find the charges (http://q4md-forcefieldtools.org/RED/). Then use

Re: [gmx-users] Density histogram in Ramachandran plot

Here in the gromacs user contribution: http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Other_software I use it once. Anthony On Thu, Nov 12, 2009 at 7:49 PM, Mark Abraham wrote: > ms wrote: >> >> Hi, >> >> I wonder if there is an easy way I am missing to get

Re: [gmx-users] Mac OS X with MKL

e this help. If you gat confused google for gromacs intel. Best regards Anthony On Wed, May 5, 2010 at 7:25 PM, Anthony Cruz Balberdi wrote: > Sorry for my bad english... That happens to me but in linux. If you are using > mkl >= 10 you need to change the way the libraries are called. Sear

Re: [gmx-users] Help, Errors while compiling gromacs under Mac OS X 10.5 Leopard

The mac computer is a cluster or just your personal computer? If you will use it to prepare the system and for analysis you could use macport or fink to compile gromacs. Anthony On Tue, May 11, 2010 at 11:13 AM, Emily Curtis wrote: > Dr. Bonner, > I am trying to install gromacs on a mac.  I am r

Re: [gmx-users] acetonitrile from amber to gromacs

I did it for other solvent. If you have AMBER is very easy to do. Do you have AMBER? On Wed, May 19, 2010 at 12:15 PM, vedat durmaz wrote: > > hi all together, > > this week i'm trying to do some simulations with acetonitrile (AN) as a > solvent and using ffamber99 as force field. on this website

[gmx-users] continuation problem

Hi: I am running a simulation (on GROMACS 3.3.1) were I want to save the coordinates of a group of atoms every steep. I use the nstxtcout and xtc_grps options in my MDP file. The problem is that when I continue the simulation (using tpbconv -f -e -s -until) the first 100 to 500 ps the coordina

[gmx-users] rerun question

HI Users: I want to rerun my system to determine the energy of the protein. What I need to do? If the answer is to set up energygrp_excl I could include all the component of the system except the protein in one group an use this group for the energygrp_excl because my system have 6 differe

[gmx-users] LJ question

Hi User: I have a little question about the LJ parameters. If I download a molecular topology from the site that have new atom types with new LJ parameters, I supposed to add an [ atomtypes ] section to the topology that define the new types and the new LJ. The question is I need to add the

[gmx-users] mixing for new LJ parameters

Hi User: I have a little question about the LJ parameters. If I download a molecular topology from the site or build a new molecule from parameters in the literature that have new atom types with new LJ parameters, how the combinations of LJ parameters will be done between this new LJ and the a

[gmx-users] pdb2gmx and his-heme group

Hi user: Today I have been working with a heme protein and I notice that in the topology the parameters that include the His (NE2) and the heme (FE) were not present in the topology (bon type, angle type, etc). Also when I check the topology after grompp (-pp) this file also do not include t

Re: [gmx-users] Appropriate tool to get the number of solvent molecules within a cutoff distance around protein molecule

Hi Ozge: You can use a script in VMD to do the work. In VMD you could make various atom selection and use it in the script. You could use something like this: set outfile [open sol_within_prot.dat w]; set nf [molinfo top get numframes] set frame0 [atomselect top "protein" frame 0] # water calcul

[gmx-users] g_sas -or

Hi: I am using the g_sas with the -or option . The output file have 3 colums: first the res number, second the sasa value, third I dont know. To what corresponds the third columnin the file? Best regards Anthony - Antes ahora