Re: [gmx-users] How to put more solutes into the system ?

Chih-Ying Lin wrote: Hi I have a system - solutes with water. The system has been under MD simulation for 100 ns. Now, I want to put more solutes in it. Would you please tell me which command can make it ? Go back to the start, take a coordinate file with a suitable periodic box defined (edit

[gmx-users] How to put more solutes into the system ?

Hi I have a system - solutes with water. The system has been under MD simulation for 100 ns. Now, I want to put more solutes in it. Would you please tell me which command can make it ? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-

Re: [gmx-users] how to obtain corresponding conformation for each point in the 2-D projection

Dear Mr Tsjerk Wassenaar : Thank you for your help! I only study on conformation transfromation (transformation) of protein, and need point to corresponding conformation in 2d projection or free energy landscape! I have no any script, please help me! Best regards! --- 09年12月22日，周二, Tsjerk

Re: [gmx-users] superimposed structures

leila karami wrote: Dear Mark *(1)* I did following steps for obtaining superimposed structure: I obtained 0.gro and 5000.gro files by above command trjconv -f *.xtc -s *.tpr -o n.gro -dump n-1

Re: [gmx-users] A problem with a "detaching Calpha/s"

Arik Cohen wrote: Dear GROMACS users, While running a simple MD simulation with both a small protein such as BPTI and a larger one such as tmRBP_Unliganded_2FN9.pdb, I'm encountering an odd situation in which one (in the case of BPTI) or several Calphas (in the later case) are "detaching them

Re: [gmx-users] trjconv -pbc: how to keep all parts of the system "clustered" together in PDB?

Visvaldas K. wrote: Dear GROMACS users and gurus, I am sorry if it's a stupid question...I'm fairly new GROMACS, and something is been driving me crazy. I have a protein, two metal ions, and inhibitor in my system. Somehow in some of the frames I can't keep all those pieces "clustered" compac

[gmx-users] A problem with a "detaching Calpha/s"

Dear GROMACS users, While running a simple MD simulation with both a small protein such as BPTI and a larger one such as tmRBP_Unliganded_2FN9.pdb, I'm encountering an odd situation in which one (in the case of BPTI) or several Calphas (in the later case) are "detaching them selfs" from the m

Re: [gmx-users] help

ashish pandey wrote: I wan to make top fil fo my complex having membrane, protein and ion. When I use x2top, I took the following error: x2top does not work for complex systems. you will need to run pdb2gmx on the protein, and do manual work for the lipids. check archives. Can not find for

Re: [gmx-users] Solvent Accessible Area with different Claculation Groups

Hi, let me add some information here to clarify the problem we're facing: >>> I was wondering if anyone has some insight on why the two sasa values are >>> not identical. >>> >>  From g_sas -h: >> >> "The calculation group should always consists of all the non-solvent atoms >> in the system. The

[gmx-users] trjconv -pbc: how to keep all parts of the system "clustered" together in PDB?

Dear GROMACS users and gurus, I am sorry if it's a stupid question...I'm fairly new GROMACS, and something is been driving me crazy. I have a protein, two metal ions, and inhibitor in my system. Somehow in some of the frames I can't keep all those pieces "clustered" compactly for some postproc

Re: [gmx-users] help

ashish pandey wrote: I wan to make top fil fo my complex having membrane, protein and ion. When I use x2top, I took Using x2top is not appropriate here. Might I recommend: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html -Justin the follo

[gmx-users] implicit solvent

Hi, Of previous discussions on the list and the wiki I conclude one can do implicit solvent simulations in GROMACS with the latest git version, but that for the moment it is rather slow. I would like to test something and it is not really a problem that the code is slow. So I guess I could use GR

[gmx-users] help

I wan to make top fil fo my complex having membrane, protein and ion. When I use x2top, I took the following error: Can not find forcefield for atom OH2-12939 with 2 bonds Can not find forcefield for atom OH2-10618 with 2 bonds Can not find forcefield for atom OH2-10621 with 2 bonds Can not find

Re: [gmx-users] g_mindist -or inconsistencies with atom-pairs

Dear Shay, What do you get when -or is present? Do the atoms always belong to the same residues? I suspect that since the calculation of the minimal distance is made for all residues, what you get at the end is the atoms at minimal distance between the last two residues. This seems like a bug and

[gmx-users] g_mindist -or inconsistencies with atom-pairs

Dear Gromacs users, We used g_mindist analysis as follows: g_mindist -f *.xtc -s *.tpr -o atom-pairs.out -od mindist.xvg -or res_mindist.xvg and surprisingly in the atom-pairs.out only several atoms in one residue (from group 1) were at minimum distance from group 2 throughout the entire

[gmx-users] superimposed structures

Dear Mark *(1)* I did following steps for obtaining superimposed structure: I obtained 0.gro and 5000.gro files by above command trjconv -f *.xtc -s *.tpr -o n.gro -dump n-1 I concatenated 2 input files ( 0.gro and 5000.gro). trjcat -f 0.gro 5000.gro -o f.xtc finally, trjconv -f f.xtc -s *.

[gmx-users] calculation of chemical shift anisotropy

Dear all,     I have simulated a small peptide on lipid-water interface under NPT condition. Is it possible to calculate the chemical shift anisotropy of the peptide from the simulation trajectory? Moutusi Manna The INTERNET now has a personality. YOURS! See your Yahoo! Homepag

Re: [gmx-users] steered MD simulation for calculating the PMF

lammps lammps wrote: Hello, I want to use the Steered molecular dynamics simulations to calculate the PMF with Gromacs. How could I write the pull code? Are there some examples? There are some in the list archives that people have posted. And what files the GMX will create when running

Re: [gmx-users] how to obtain corresponding conformation for each point in the 2-D projection

Ni hao Xi Zhao, Please note again that you're working with projections. There is not necessarily a single conformation that corresponds to the energy minimum from your projection space. You can obtain the minimum from the 2D projection and then find the conformation that yields the projection clos

Re: [gmx-users] superimposed structures

leila karami wrote: Hi I used commands trjconv and trjcat for fitting and obtaining of superimposed structure between initial and final structure You're much more likely to get any feedback if you tell us your command lines. I've lost track of the number of times I've said this to you so

[gmx-users] steered MD simulation for calculating the PMF

Hello, I want to use the Steered molecular dynamics simulations to calculate the PMF with Gromacs. How could I write the pull code? Are there some examples? And what files the GMX will create when running the SMD code? Then how to obtain the PMF after full running? Is there any command for this?

[gmx-users] superimposed structures

Hi I used commands trjconv and trjcat for fitting and obtaining of superimposed structure between initial and final structure but when I open pdb file containing superimposed structure with VMD, 2 structures were shown but there is some exessive bonds. I did following works but problem was not s