[gmx-users] Energy Calculation

Hi! I want to calculate energy from GROMOS96-GB/SA. What command should be used? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe

Re: [gmx-users] value of an angle

Hi, if you are interested in a particular angle (between a triad of atoms) you can specify it in angle.ndx file (to generate the angles run: mk_angndx -s topol.tpr -n angle.ndx) the -ov flag of g_angle will generate the angle trajectory and the -od flag will generate its distribution cheers On

Re: [gmx-users] Energy Calculation

simon sangma wrote: Hi! I want to calculate energy from GROMOS96-GB/SA. What command should be used? g_energy -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech

[gmx-users] System has non-zero total charge: -8.000001e+00

IS this a problem? *System has non-zero total charge: -8.01e+00* If yes, can I fix that changing COulomb cutt-off to PME electrostatics? THanks!! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gr

Re: [gmx-users] System has non-zero total charge: -8.000001e+00

Maurício Menegatti Rigo wrote: IS this a problem? /System has non-zero total charge: -8.01e+00/ If yes, can I fix that changing COulomb cutt-off to PME electrostatics? You need to add counterions to your system. Consult some basic tutorial material, as well as the manual entry for gen

[gmx-users] Steered Molecular Dynamics (SMD)

Dear all: These days, I am trying to pull a slab of griphene moving along the Z direction at a constant speed. The slab of griphene contains 700 atoms. After several times of E-mail communication with the Gromacs users, the simulation can run. However, the run didn't produce the results which I

Re: [gmx-users] System has non-zero total charge: -8.000001e+00

You should always neutralise your sysem. On Thu, Feb 25, 2010 at 1:42 PM, Maurício Menegatti Rigo < mauriciomr1...@gmail.com> wrote: > IS this a problem? > > *System has non-zero total charge: -8.01e+00* > > If yes, can I fix that changing COulomb cutt-off to PME electrostatics? > > THanks!!

[gmx-users] energy minimization problem

Hi , I have a protein with 2 chains. I need to do normal mode analysis on it. As there are no covalent bonds between the two chains, I did not use the "merge" option in the "pdb2gmx" command. I am trying to energy minimize the structure , in vaccum.( in double precision) , but am not a

[gmx-users] Order parameter for unsaturated lipid chain in UA model

Dear gmx users, I am sorry to ask this question again, but reading in the email achieve did not enlighten me. I found this email which describes my problem, but unfortunately it has no replies: http://lists.gromacs.org/pipermail/gmx-users/2008-July/034950.html Also there are these two rece

Re: [gmx-users] Order parameter for unsaturated lipid chain in UA model

Sarah Witzke wrote: Dear gmx users, I am sorry to ask this question again, but reading in the email achieve did not enlighten me. I found this email which describes my problem, but unfortunately it has no replies: http://lists.gromacs.org/pipermail/gmx-users/2008-July/034950.html Als

SV: [gmx-users] Order parameter for unsaturated lipid chain in UAmodel

Thank you for your quick respons! It is not so much the drop, but more the position and the prescens of a small drop, then a little rise and then the big drop. I have pasted the file in below. Do you think my method of replacing the order parameters for the double bonded atoms is ok? *

Re: [gmx-users] value of an angle

Thank you for your replies, indeed it worked! But now, I'm looking for a command line that allows me to calclulate the RMSF (or if you prefer, the distance between Calpha) between 2 static structures. Carla On Thu, Feb 25, 2010 at 11:55 AM, Amir Marcovitz wrote: > Hi, > > if you are interested i

Re: [gmx-users] value of an angle

On 26/02/2010 1:11 AM, Carla Jamous wrote: Thank you for your replies, indeed it worked! But now, I'm looking for a command line that allows me to calclulate the RMSF (or if you prefer, the distance between Calpha) between 2 static structures. Look in section 7.4 of the manual for a run-down on

Re: SV: SV: [gmx-users] Order parameter for unsaturated lipid chain in UAmodel

Sarah Witzke wrote: Thank you for looking at the data. I just thought, that it deviated too much from published results, but perhaps it is because I have mainly worked with saturated lipids. I calculated the order over the last 117 ns of a 167 ns trajectory (10 ps between each frames), so there

[gmx-users] problem with freezing group size

Dear all, I am sorry for poorly describing my problem about the freezing group size. Here I am giving my question very briefly, can anybody help me please? I would like to know the relation between the size of freezing group and the temperature coupling. when I separate the temperature coupling f

RE: [gmx-users] energy minimization problem

Actual text input / output would be a good idea here. What is the actual output when you try to run it the second time? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dall

[gmx-users] query about free energy landscape

Dear Sir,     I am facing one problem regarding generation of Free energy landscape (FEL); I have some doubt regarding the algorithm of g_sham. I will be highly obliged if you kindly let me clear my doubt. I know that three variables are needed for construction of 3D energy landscape.

[gmx-users] POPC Membrane + protein dynamics

Dear All, I'm a new comer to gromacs. I need to perform molecular dynamics simulation of my protein within the POPC membrane. I have downloaded the 128a popc lipid from Prof.Tieleman's group along with the required popc.itp. My protein of interest is 458 residues. Since the 128a popc is already Sim