Re: [gmx-users] Gibbs free energy of binding

Dear Gromacs users I want to calculate Gibbs free energy too,but about Protein-drug binding. Please guide more clearly,what texts I need to read for learning how can I do it? Besides,g-energy has an option for estimating free energy from trajectory file(-fee option) I thought if I had a

Re: [gmx-users] g_dipole ? = what is the bond length of the ionic bond in the dipole moment calculation?

On 2010-10-20 06.06, Chih-Ying Lin wrote: Hi molecule dipole is 48.0 sum of q_i x_i x_i the bond length for covalent bond. No. x_i is the atomic position. but what is x_i for salt-molecule? For salt-molecule, the ionic bonds are broken in water solvent and the counter ions are spread

Re: [gmx-users] top2psf.pl is generating some bonds to atoms with index 0.

Alright.. I actually simulated my protein for 5ns. Then I loaded the trajectory file and .gro file in vmd. Then, I extracted one of the frame and write it into pdb format, When I open it with vmd, one of the atom from a residue is connected to another atom in another residue. Things like this

Re: [gmx-users] Error on install Gromacs 4

On Oct 20, 2010, at 5:17 AM, Son Tung Ngo wrote: Dear experts, I have just install gromacs 4.5.1 on my cluster (using CentOS that was install openmpi1.5, Platform MPI, fftw3, g77, gcc , g++) but I have problem with size of int : [r...@icstcluster gromacs-4.5.1]# ./configure

Re: [gmx-users] Re: Template file in gromacs4.5.1

On Tue, Oct 19, 2010 at 4:14 PM, Sikandar Mashayak symasha...@gmail.com wrote: Now I have upgraded to gromacs4.5.1 and when I check its template file , its completely different that the earlier version. Does that mean old post-processing codes have to rewritten if I were to use new gromacs?

Re: [gmx-users] -pbc nojump

On 20/10/2010 9:07 PM, leila karami wrote: Hi gromacs users I study simulation of protein-dna interaction using gromacs. After full md simulation, because of diffusion of one strand of dna to edge of box, I used trjconv -f old.xtc –o new.xtc –s *.tpr -pbc nojump -ur compact –center. By

[gmx-users] -pbc nojump

Dear Mark thanks for your attention when I used trjconv -pbc nojump, I made one group (protein and dna) in index file and I selected that as centering group. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] -pbc nojump

On 20/10/2010 9:24 PM, leila karami wrote: Dear Mark thanks for your attention when I used trjconv -pbc nojump, I made one group (protein and dna) in index file and I selected that as centering group. What is the problem? :-) You might need two passes with trjconv. Mark -- gmx-users

[gmx-users] -pbc nojump

Dear Mark my mean of [when I used trjconv -pbc nojump, I made one group (protein and dna) in index file and I selected that as centering group.] is that the problem (nonentity of water molecules in interface of protein and dna) was not solved. what is your mean of [You might need two passes with

Re: Fwd: [gmx-users] Hardware-specific crash with 4.5.1

Please keep all Gromacs-related correspondence on the gmx-users list, and do not hijack an old, unrelated thread to ask questions. I am CC'ing the list and I would ask that all further discussion take place there. I have no answer to your question, aside from advising you to read the

Re: [gmx-users] -pbc nojump

On 20/10/2010 9:55 PM, leila karami wrote: Dear Mark my mean of [when I used trjconv -pbc nojump, I made one group (protein and dna) in index file and I selected that as centering group.] is that the problem (nonentity of water molecules in interface of protein and dna) was not solved. what

Re: [gmx-users] Gibbs free energy of binding

mohsen ramezanpour wrote: Dear Gromacs users I want to calculate Gibbs free energy too,but about Protein-drug binding. Please guide more clearly,what texts I need to read for learning how can I do it? Look into the literature and nearly any of the popular simulation textbooks.

Re: [gmx-users] top2psf.pl is generating some bonds to atoms with index 0.

Kwee Hong wrote: Alright.. I actually simulated my protein for 5ns. Then I loaded the trajectory file and .gro file in vmd. Then, I extracted one of the frame and write it into pdb format, When I open it with vmd, one of the atom from a residue is connected to another atom in another

[gmx-users] -pbc nojump

Dear Mark you said in answer to -pbc nojump that using of new xtc file for analysis section depends what one wants to observe. what observations is relevant to periodicity? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

Re: [gmx-users] Gibbs free energy of binding

Dear Justin You are right,But I searched in tools and I found g_sham It is very useful tool for estimating Gibbs free energy,Enthalepy , emtropy and ... I think I can use from that for my calculation of binding free energy(In the other words,del G free energy of system ) how do you think about

Re: [gmx-users] Gibbs free energy of binding

mohsen ramezanpour wrote: Dear Justin You are right,But I searched in tools and I found g_sham It is very useful tool for estimating Gibbs free energy,Enthalepy , emtropy and ... I think I can use from that for my calculation of binding free energy(In the other words,del G free energy of

Re: [gmx-users] Reg: Running Energy minimisation for dichloroethane (DCE)

vinothkumar mohanakrishnan wrote: Hi Justin I corrected the mistake what you said and i am able to run energy minimisation and equilibration. but when i view my em.gro and equilibration.gro in VMD it seems to me that the bonds between the atoms are broken in molecules.I used g_energy to

[gmx-users] Force-field files location and order of reading in Gromacs 4.5.2

Hi all, I have detected that preference in reading forcefield files in Gromacs 4.5 has probably been changed from Gromacs 4.0.x and older. In older gromacs, when there was forcefield with modification present in my working directory, then it was read preferentially, but now it seems that

Re: [gmx-users] Force-field files location and order of reading in Gromacs 4.5.2

Karel Berka wrote: Hi all, I have detected that preference in reading forcefield files in Gromacs 4.5 has probably been changed from Gromacs 4.0.x and older. In older gromacs, when there was forcefield with modification present in my working directory, then it was read preferentially, but

Re: [gmx-users] -pbc nojump

On 20/10/2010 10:26 PM, shahab shariati wrote: Dear Mark you said in answer to -pbc nojump that using of new xtc file for analysis section depends what one wants to observe. what observations is relevant to periodicity? Anything that measures where something is relative to another.

[gmx-users] Gromacs build error

Hello, I am trying to build Gromacs 4.5 from source using the Portland Group compiler: [r...@master1 gromacs-4.5]# echo $CPPFLAGS -I/cvos/shared/apps/fftw/pgi/64/3.1.2/include [r...@master1 gromacs-4.5]# echo $LDFLAGS -L/cvos/shared/apps/fftw/pgi/64/3.1.2/lib [r...@master1 gromacs-4.5]# echo $CC

Re: [gmx-users] Gromacs build error

Hi, I am trying to build Gromacs 4.5 from source using the Portland Group compiler: Have you tried adding -Mm128 to CFLAGS? A. -- Ansgar Esztermann DV-Systemadministration Max-Planck-Institut für biophysikalische Chemie, Abteilung 105 -- gmx-users mailing listgmx-users@gromacs.org

RE: [gmx-users] Gromacs build error

Hello Ansgar, What does this switch do? When I do set the variable, it cannot even create the Makefiles: [r...@master1 gromacs-4.5]# ./configure --enable-shared --enable-double --enable-mpi --prefix=/cvos/apps/gromacs-4.5 --program-suffix=_mpi_d checking build system type...

Re: [gmx-users] Gromacs build error

Hi, What does this switch do? When I do set the variable, it cannot even create the Makefiles: According to the manpage, it enables the __m128 types. The original error message points to a line containing such a type. I've looked at the PGI 10.3 manpage -- other versions may behave

Re: [gmx-users] Gromacs build error

On Wed, 2010-10-20 at 16:37 +0200, Esztermann, Ansgar wrote: Hi, What does this switch do? When I do set the variable, it cannot even create the Makefiles: According to the manpage, it enables the __m128 types. The original error message points to a line containing such a type.

[gmx-users] FEP Calculation problem on GMX 4.5.1

Hello! I am new to this list, probably someone has have the same problem I am facing now with the use of Gromacs to calculate FEP (Free energy pertubaion). I've followed the gromacs tutorial for Free energy Calculation available at

Re: [gmx-users] FEP Calculation problem on GMX 4.5.1

On October 20, 2010 at 9:22 PM Marcelo Brando brandao.marc...@gmail.com wrote: Hello! I am new to this list, probably someone has have the same problem I am facing now with the use of Gromacs to calculate FEP (Free energy pertubaion).

Re: [gmx-users] FEP Calculation problem on GMX 4.5.1

TJ Mustard wrote: On October 20, 2010 at 9:22 PM Marcelo Brandão brandao.marc...@gmail.com wrote: Hello! I am new to this list, probably someone has have the same problem I am facing now with the use of Gromacs to calculate FEP (Free energy pertubaion). I've followed the

[gmx-users] question about periodic boundary conditions

Hi, Is there a way to quantitatively determine, from a trajectory file, whether a molecule is interacting with a copy of itself in the adjacent box (given that PBC is applied)? Currently, I'm using VMD - I've already loaded the *xtc file into the*gro structure file and viewed the periodic images

Re: [gmx-users] question about periodic boundary conditions

rainy...@yahoo.com wrote: Hi, Is there a way to quantitatively determine, from a trajectory file, whether a molecule is interacting with a copy of itself in the adjacent box (given that PBC is applied)? Currently, I'm using VMD - I've already loaded the *xtc file into the*gro structure

Re: [gmx-users] question about periodic boundary conditions

rainy...@yahoo.com wrote: Hi Justin, Thanks for getting back to me. I executed the following command using g_mindist: $gromacs/g_mindist -pi -f n12_random_all.xtc -s n12_random.tpr -n index.ndx -od mindist.xvg ..and got the output (see below). It shows that the minimal distance to

Re: [gmx-users] FEP Calculation problem on GMX 4.5.1

I would have this in my production mdp files, or something like it: ; Free energy control stuff free-energy = yes ; = no init-lambda = XXX ; = 0 delta-lambda = 0 ; = 0 foreign_lambda = ; = sc-alpha = 0.5 ; = 0 sc-power = 1.0 ; = 0 sc-sigma =

Re: [gmx-users] question about periodic boundary conditions

Justin, I have a single solute. But I understand what you're saying about the cutoff. My long-range cutoff is set to 1.2 nm (from MARTINI force field), so therefore, the snapshots corresponding to a minimum periodic distance of 1.2 nm would agree with the overlap witnessed in VMD? Thanks

Re: [gmx-users] question about periodic boundary conditions

rainy...@yahoo.com wrote: Justin, I have a single solute. But I understand what you're saying about the cutoff. My long-range cutoff is set to 1.2 nm (from MARTINI force field), so therefore, the snapshots corresponding to a minimum periodic distance of 1.2 nm would agree with the

[gmx-users] g_dipole ? = salt molecule in water = what is the the displacement vector pointing from the negative charge to the positive charge?

Hi molecule dipole is 48.0 sum of q_i x_i based on the following two websites, *x_i * is the displacement vectorhttp://en.wikipedia.org/wiki/Displacement_%28vector%29pointing from the negative charge to the positive charge. what about the x_i for the salt-molecule, which dissociates into one

Re: [gmx-users] question about periodic boundary conditions

Hi, I am new to the list. I am trying to simulate lipid bilayer with atomistic model. I want to calculate surface pressure at phase boundary. I am thinking of using #surf*surfTen option with g_energy. But I am afraid, that I won't get a meaningful value because of large fluctuations.

[gmx-users] g_dipole ? = salt molecule in water = should I include counter ions in my calculation?

HI 48.0 sum of q_i x_i x_i is the atomic position. For the salt molecule in water, should I include counter ions in my calculation ? Or, only the rest of the salt molecule except the counter ions? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] question about periodic boundary conditions

On 21/10/2010 10:45 AM, Abhijeet Joshi wrote: Hi, I am new to the list. I am trying to simulate lipid bilayer with atomistic model. I want to calculate surface pressure at phase boundary. I am thinking of using #surf*surfTen option with g_energy. But I am afraid, that I won't

[gmx-users] Re: Re: swiss param query

Hi all, Just as a follow-up on this one: the problem was solved by a correct ordering of the sections in the topology. The SwissParam server (www.swissparam.ch ) works correctly to generate Gromacs topologies for small organic molecules! Note that the tutorial has been updated for the

[gmx-users] Surface pressure for lipid bilayer.

Hi, As correctly pointed out by Mark, I am restating my concern in this topic. I am trying to simulate lipid bilayer with atomistic model. I want to calculate surface pressure at phase boundary. I am thinking of using #surf*surfTen option with g_energy. But I am afraid, that I

[gmx-users] g_dipole ? = The salt molecule = The discrepancy of dipole moment between my calculation and GROMACS

HI dipole moment = 48.0 sum of q_i x_i x_i is the atomic position. I did not include the counter ion of the salt molecule in my calculation. The salt molecule is A-N(CH3)3-Br and it has two structures, cis and trans. Here A are a string of atoms, most of them are carbons. For the cis-structure