[gmx-users] how to get a minimized structure pdb

Dear Users ! I have done a minimization for a tetrapeptide in a water box with conjugate gradient minimization of 1000 steps when I convert it to pdb as below trjconv -f em.trr -o min.pdb -s em.tpr << EOF 0 EOF the out put pdb has many structures as follo

[gmx-users] how to get a minimized structure pdb

Dear Users ! I have done a minimization for a tetrapeptide in a water box with conjugate gradient minimization of 1000 steps when I convert it to pdb as below trjconv -f em.trr -o min.pdb -s em.tpr << EOF 0 EOF the out put pdb has many structures as follo

[gmx-users] energy_terms

Dear Users I have a peptide, (1AKI.pdb) My aim is to solvate it in the presence of the explicit water molecules and do minimization and to split the energy terms , and to see the energy contribution from each terms for this i have done the following in gromacs -

RE: [gmx-users] energy_terms

On 17/12/2011 5:25 PM, balaji nagarajan wrote: Dear Users ! I have used the energy group option to split the energy terms , for the protein and the water. You have split the *non-bonded* terms

[gmx-users] energy_terms

Dear Users ! I have used the energy group option to split the energy terms , for the protein and the water. It gives all the terms , protein-protein , water-water , water-protein . I have a doubt , the distance and the angle are taken for both water and the protein , how one can get the

[gmx-users] problem_with_rewritting_pdb

Dear Users ! I have minimized the attached file using the gromacs43a1 and oplsaa force field using spc water molecules I have used the following script for generating topology . i minimized for 2000 steps , my doubt is when i rewrite the minimized pdb , in case of oplsaa i was able to get

RE: [gmx-users] topology_for_3 point model

:02:04 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] error_in topology > > > > balaji nagarajan wrote: > > Dear Users ! > > > > I have a problem in generating the topology of the attached molecule as pdb. > >

[gmx-users] error_in topology

Dear Users ! I have a problem in generating the topology of the attached molecule as pdb. earlier i have done using the same pdb for solvating the structure using spc and spce water box , there was no such error when i do for TIP4P and oplsaa force field i got the error as follows -

[gmx-users] free energy

Dear Users ! Is it possible to calculate the free energy for a molecule , at the zero step MD , when i see the mail list this question has been posted once , but i could not find the reply for this ! is there any option for this like g_energy !

[gmx-users] minimization_error

Dear Users ! I have a doubt in minimizing the structure with water box ! I have taken a penta peptide and solvated it with spce water box ! I have minimized the system with the minim.mdp file which i have attached ! ( i have used steep option ) when I calculated the protein- protein and

[gmx-users] final_min_step energy

Dear Users ! I have a problem in taking the inter and intra molecular interaction energy from a pdb , which is being minimized by minim.mdp ! when i use the g_energy -f *.edr it gives the list of all possible interaction energy as average value , but i want it only for the minimized f

[gmx-users] Mu-X

Dear Users ! I have done the g_energy using the *.edr file ! In that it prints all the energy terms , i can understand most of the terms ! i dont know what does Mu-X , Mu-Y , Mu-Z represents and its importance ! I would like to know the detail of the force fields included in the gromacs !

RE: [gmx-users] interaction energy

ct: Re: [gmx-users] interaction energy > > > > balaji nagarajan wrote: > > > > > > > > Dear Users ! > > > > i would like to do this to a set of files ! > > so how to print the required values in the text mode or is there any > > fla

RE: [gmx-users] interaction energy

ct: Re: [gmx-users] interaction energy > > > > balaji nagarajan wrote: > > Dear Users ! > > > > Now i am able to do the protein solvent interaction ! > > > > thanks ! i have understood ! > > > > when i used the energygrps , > > wh

[gmx-users] interaction energy

Dear Users ! Now i am able to do the protein solvent interaction ! thanks ! i have understood ! when i used the energygrps , when i used the g_energy -f em.edr this command it prints all terms and asks to make selection as below, 1 Bond 2 Angle3 Proper-Dih.

[gmx-users] solvent_protein interaction energy

Thanks for the reply ! I have tried building the topology with generating the index file make_ndx -f * it gave options i have selected the protein and the solvent then i gave minimization in the minimization file i have included energygrps = Protein SOL , but the energy file ha

[gmx-users] energy_extract

Dear Users ! I have took a penta peptide and did topology generation , I have solvated it with water box , now i did a minimization with zero step , to know the energy of the initial molecule , i used g_energy for the out put , like $ g_energy -f em.edr it gives as follows , i have to

[gmx-users] terminal_fixing

Dear Users ! i have tried in generating the -ter option in generating the topology file ! it asks the below if i give the ter option , Select start terminus type for TYR-1 0: NH3+ 1: ZWITTERION_NH3+ 2: NH2 3: None then if i give option 1 it chooses ZWITTERION_NH3+ , i want to make the

[gmx-users] print inter and intra energy

Dear users ! I am new to gromacs ! I have installed the package ! and it is working fine ! I tried to solvate a peptide and i was able to select the force field of my interest , I would like to calculate the energy of the structure in terms of inter and intra and i want to print all th