[gmx-users] estimate free energy bu LIE method, about long range electrostatic interaction

Dear All: I would like to estimate the binding free energy between a drug molecule and its receptor. Inorder to do this, i run a MD simulation in which PME method was used to deal with long range electrostatic interaction. I need to calculate the VDW interaction energy and

[gmx-users] about estiminating the binding free energy by LIE method

Dear All: I would like to estimate the binding free energy between a drug molecule and its receptor. Inorder to do this, i run a MD simulation in which PME method was used to deal with long range electrostatic interaction. I need to calculate the VDW interaction energy and

[gmx-users] Problem in applying postion restrain on protein

Hello Justin sir sorry , The suggestion U given to me is not working. Actually I am a master student and just started to do simulation of membrane protein . Here no one did this work thats why i am facing more problem. sorry for putting question all the time in gmx-user list . But its

Re: [gmx-users] Problem in applying postion restrain on protein

nitu sharma wrote: Hello Justin sir sorry , The suggestion U given to me is not working. Actually I am a master student and just started to do simulation of membrane protein . Here no one did this work thats why i am facing more problem. sorry for putting question all the time in

[gmx-users] Re: Questions

Hi Lin, 1. Although you have explained the differece between HOH, AHOH and BHOH, I do not fully understand.     = Can I delete all of atoms, HOH, AHOH and BHOH ? You can delete one of them, either A or B, if you want to include the water in your model. It may be that pdb2gmx discards the B

RE: [gmx-users] what is meaning of vol 0.95 imb F 1%?

Date: Thu, 30 Apr 2009 11:33:24 +1000 From: mark.abra...@anu.edu.au To: gmx-users@gromacs.org Subject: Re: [gmx-users] what is meaning of vol 0.95 imb F 1%? wuxiao wrote: Dear gmx users, If -v was passed on to mdrun, such rows one by one would be printed continuously as

[gmx-users] md error message

Dear all, I am trying to do an md simulation of a system consiting of water and liquid crystalline molecules, starting from a random initial configuration. After some energy minimization if I try to do an NVT simulation (I use the VERSION 4.0.3) I get the error t = 0.000 ps: Water molecule

Re: [gmx-users] md error message

Antonia V. wrote: Dear all, I am trying to do an md simulation of a system consiting of water and liquid crystalline molecules, starting from a random initial configuration. After some energy minimization if I try to do an NVT simulation (I use the VERSION 4.0.3) I get the error Please

[gmx-users] Conjugate Gradient - Equations

Hi everyone, In the gromacs manual the equations regarding the conjugate gradient are not shown. Is there anybody that can help me find them or send them to me? Cheers, Una ___ gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Error by pdb2gmx

Hi, Dallas: I added this to the ffoplsaa.rtp [ PDM ] [ atoms ] SI SI 0.300 1 CH3 opls_0690.000 1 O opls_108 -0.300 1 [ bonds ] SI O SI CH3 [ dihedrals ] CH3SIO SI dih_PDM_chi1_C_SI_O_SI

[gmx-users] estimate the binding free energy. long range electrostatic interaction

mirc...@sjtu.edu.cn wrote: Dear All: I would like to estimate the binding free energy between a drug molecule and its receptor. Inorder to do this, i run a MD simulation in which PME method was used to deal with long range electrostatic interaction.

Re: [gmx-users] Error by pdb2gmx

Yanmei Song wrote: Hi, Dallas: I added this to the ffoplsaa.rtp [ PDM ] [ atoms ] SI SI 0.300 1 CH3 opls_0690.000 1 O opls_108 -0.300 1 [ bonds ] SI O SI CH3 [ dihedrals ] CH3SIO SI

Re: [gmx-users] Error by pdb2gmx

Hi, Justin: Thank you so much for your nice help. I will work on that according to your suggestions. On Thu, Apr 30, 2009 at 10:46 AM, Justin A. Lemkul jalem...@vt.edu wrote: Yanmei Song wrote: Hi, Dallas: I added this to the ffoplsaa.rtp [ PDM ] [ atoms ]      SI       SI            

[gmx-users] Coarse graining for Benzene and related molecules

Hi all, I want to simulate a molecule which has many benzene rings attached to each other. However I want to coarsegrain the system a lot !! I want to represent the center of masses of benzene rings with point masses. For all the parameters, such as bonds, angles, dihedrals I can use similar

[gmx-users] energy xvg file shows a large energy change from time step 0 to time step 0.2 ps

Hi! I have just completed a position restrained dynamics run on my protein with GROMACS 3.3.3 and I generated an xvg file with the g_energy command...I noticed in this that the energy for time step 0 was 0.88 (near 0) kj mol/S-1/N while the energy for time step 0.2ps was 1158after this the

Re: [gmx-users] Error by pdb2gmx

That means both the rtp and pdb files work in your GROMACS-4.0.4. For the issue of PDME residue has a net +0.3 charge , I should change the charge to 0 for Si in PDME, which I have ignored. I will update the software and see if it works. Thanks so much for your help! On Thu, Apr 30, 2009 at

[gmx-users] configuration does not change in minimization trajectory

Hello all, I am doing a cg minimization with Gromacs-4.0.3. It is compiled on a Linux system with gcc 3.4.6 All frames in the trajectory are identical to the starting configuration, except for the final one, which is clearly different. I get the expected number of frames in the trajectory

Re: [gmx-users] configuration does not change in minimization trajectory

heiko...@web.de wrote: Hello all, I am doing a cg minimization with Gromacs-4.0.3. It is compiled on a Linux system with gcc 3.4.6 All frames in the trajectory are identical to the starting configuration, except for the final one, which is clearly different. How are you assessing this?

Re: [gmx-users] energy xvg file shows a large energy change from time step 0 to time step 0.2 ps

hi, It will be better to check the energy after the final production run Pawan On Fri, May 1, 2009 at 12:15 AM, Halie Shah halieps...@gmail.com wrote: Hi! I have just completed a position restrained dynamics run on my protein with GROMACS 3.3.3 and I generated an xvg file with the