[gmx-users] pdo making

files to do this analysis but I can not find any option -pd in this version of gromacs in mdrun command. What can I do to make pdo file in this version of gromacs? Thank you in progress Parto Haghighi -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx

[gmx-users] gibbs+umbrella+constraint

Dear gmx users I am working on an umbrella sampling system.(lipid bilayer+drug). I have used distance here is my mdp file for pulling: title = Umbrella pulling simulation define = -DPOSRES_LIP ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 250 ;

[gmx-users] umbrella curve

Dear gmx users I have done umbrella sampling for a membrnae drug system and i have used 13 windows in this process but at last when I extracted the histogram curve I only had two peak.Is this reasonable? Also my PMF curve has several minimum and maximum points and at last it converges to zero.Is i

[gmx-users] umbrella-drug

Dear Justin thank you for your response here is my umbrella part of mdp file: ; Pull code pull = umbrella pull_geometry = position ; simple distance increase pull_dim= N N Y pull_start = yes ; define initial COM distance > 0 pull_ngroups= 1 pull_group0 =

[gmx-users] umbrella-drug

Dear gmx-users I am working on lipid membrane+drug system.I should do umbrella sampling in this procedure: 1.cat drug and lipid 2.energy minimization 3.run npt 4.run md_pull I want to pull drug into the membrane but gromacs pushes the drug to the sides of box.and this result is independent of drug

[gmx-users] position restrain

Dear GMX users, I am working on lipid_drg system my drug molecule has 23 atoms. [ moleculetype ] ; Name nrexcl DRG 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CH3 1 DRG CAA 1 -0.073 15.0350 2 CH2 1 DRG CAH 2

[gmx-users] free energy (coordinates file)

Dear GMX users, I have a question about 6th gromacs tutorial. I have to perform 5 steps of calculation contain: 1) EM-1 2) EM-2 3) NVT 4) NPT 5) Product MD for each Lambda value from 0 up to 1. I have a .gro file contains initial coordinates of my system : drg.gro For lambda = 0.00 I have done 5 st

[gmx-users] free energy and charges

Dear GMX users, when I want to correct charge group of one molecule I have to do calculate its free energy. I did this work by applying 6th gromacs tutorial. In this tutorial user has to assign 0 value in topology: [ atoms ] ; nr type resnr residue atom cgnr charge mass type

[gmx-users] Charge fitting

Dear GMX usesr, I have to do charge fitting for a small molecule like ethanol. I have applied PRODRG to generate .gro and .itp for ethanol but it has wrong atomic charge. To correct it I have to use gromos 43a1 force field parameters to assign charges on each atom (Is it right?) I have red a pape

[gmx-users] Modify charge groups

Dear Justin, Thank you very much for your response. I have another question to continue my calculations. To correct charges and charge groups I have to: 1) seprate the molecule to functional groups 2) some of these functional groups are already exist in selected force field ( in aminoacid.rtp) wit

[gmx-users] TI results

Dear GMX users, I want to prepare an .itp for a new molecule ( like fifth gromacs tutorial). 1 ) I applied PRODRG to create its drg.itp. 2 ) Now I want to correct its partial atomic charge. As I have red in a paper (http://pubs.acs.org/doi/abs/10.1021/ci100335w) I have to do thermodynamic integrat

[gmx-users] EM curve question

Dear Mark, Thanks for your answer. I have done these steps: 1. Prepare ligand topology by PRODRG server (like fifth gromacs tutorial) 2. Download lipid.itp file and make new force field for it (like second gromacs tutorial) 3. Use editconf and cat to prepare a system with 12 ligand in both sides of

[gmx-users] EM curve question

Dear GMX-users I am working on lipid-drug system.I have done these stages: 1.creating topology for drug and lipid 2.solvation 3.Ion addition 4.Energy minimization 5.NVT My question is,why does the energy and temperature curves converge to zero(I have used 320 K for my temperature in mdp file)? Tha

[gmx-users] QM calculation

ry quantum mechanics calculation. It will be really your kind. Thanks a lot in advance. Parto Haghighi -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posti

[gmx-users] Partial atomic charge

Dear GMX users, I could make topology file of a ligand molecule by PRODRG but it has wrong charge on each atom and as mentioned in Gromacs tutorial (protein-ligand complex) I have used quantum mechanic calculation (like spartan) to correct its charge: .itp file from PRODRG: [ atoms ] ; nr

[gmx-users] Add ligand molecules in a lipid bilayer

Dear Dr.Abraham, Thanks a lot for your response. I have another question. Should I add several molecules in DMPC together or I should add them one by one? Best regard Parto -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the arc

[gmx-users] Add ligand molecules in a lipid bilayer

Dear gmx_users, I am working on lipid/drug molecule system. I could make the ligand topology by PRODRG and get DMPC.itp from http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies. To add ligand molecule I first changed its coordinate by: editconf -f drg.gro -o drg_newbox.gro -c -b