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 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 g_energy command..

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? Ex

[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 (.trr)

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 5:

Re: [gmx-users] Error by pdb2gmx

Your system works for me under Gromacs 4.0.4 - the only issue is that your PDME residue has a net +0.3 charge. Does your Gromacs installation work properly for proven systems like proteins? I would suggest upgrading to version 4.0.4 and trying again. If that does not work, post to the list

Re: [gmx-users] Error by pdb2gmx

Sorry to bother so many times. I edited the rtp and added the new residue as following, which I think should be no problem. [ PDM ] [ atoms ] SI1SI 0.3001 C1 opls_069 0.0001 C2 opls_069 0.0001 O1 opls_108-0.3001 [ bond

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

ROHIT MALSHE wrote: 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, dihedral

[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 res

[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

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 wrote: > > > Yanmei Song wrote: >> >> Hi, Dallas: >> >> I added this to the ffoplsaa.rtp >> >> [ PDM ] >> >> [ atoms ] >>      SI       SI      

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 dih_

[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 >> intera

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] 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 http://www.gromacs.org

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 updat

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

[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 st

Re: [gmx-users] Re:trestart

Sunil Thapa wrote: Respectable Justin/David/Mark and all other Experts Grettings I am not clear about the function of the option -trestart in g_msd With trestart =0 the msd curve is very kinky which really improves to a smooth one when trestart=1 is set. But when I increase the value to 10, 20

[gmx-users] Re:trestart

Respectable Justin/David/Mark and all other Experts Grettings I am not clear about the function of the option -trestart in g_msd With trestart =0 the msd curve is very kinky which really improves to a smooth one when trestart=1 is set. But when I increase the value to 10, 20 and 100 ps the smoo

[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] about estiminating the binding free energy by LIE method

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. > I need to calculate the

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-