[gmx-users] Re: Nitrogen box

Dear Justin, Thanks for your reply. Now, I have problem in generationg the coordination file. Since my molecule is diatomic, the PRODRG server fails and when I used another parametrization tool, the output files were void. Can I generate the file in gromacs? Is there any way to do it? Regards, Sa

Re: [gmx-users] about -CN triple bond

On 1/03/2011 4:58 PM, C.Y. Chang wrote: Hi, I have modified the dummy atom in the topology (attached files) and pdb file. On the other side, I study the lipid system. Therefore, I constrained all bond lengths in my system. This is bond parameters in the mdp file. continuation= no

Re: [gmx-users] about -CN triple bond

Hi, I have modified the dummy atom in the topology (attached files) and pdb file. On the other side, I study the lipid system. Therefore, I constrained all bond lengths in my system. This is bond parameters in the mdp file. continuation= no; starting up constraints = all-bonds

Re: [gmx-users] charge group radii- use maxwarn or increase rlist?

Thank you for your helpful comments. I am totally convinced that I was not using proper force field. Best, moeed On 28 February 2011 18:12, Justin A. Lemkul wrote: > > > Moeed wrote: > >> Dear Justin, >> >> Thank you for your message. My objective is to calculate interaction >> energies betwe

Re: [gmx-users] charge group radii- use maxwarn or increase rlist?

Moeed wrote: Dear Justin, Thank you for your message. My objective is to calculate interaction energies between polymer (polyethylene) and hydrocarbon solvent ( also FE calculations). I am using rlist of 1.1 nm. 1- Do I need to increase rlist ( to 1.4 nm) to overcome the error message?

Re: [gmx-users] charge group radii- use maxwarn or increase rlist?

Dear Justin, Thank you for your message. My objective is to calculate interaction energies between polymer (polyethylene) and hydrocarbon solvent ( also FE calculations). I am using rlist of 1.1 nm. 1- Do I need to increase rlist ( to 1.4 nm) to overcome the error message? 2- As with the electro

Re: [gmx-users] charge group radii- use maxwarn or increase rlist?

Moeed wrote: Dear experts, Please kindly comment on this error. Thank you very much. I am getting the known charge group radii error. (in 4.0.7 version with the same settings my simulations run with no error) == NOTE 1 [file md.mdp]: The sum of the two largest cha

[gmx-users] charge group radii- use maxwarn or increase rlist?

Dear experts, Please kindly comment on this error. Thank you very much. I am getting the known charge group radii error. (in 4.0.7 version with the same settings my simulations run with no error) == NOTE 1 [file md.mdp]: The sum of the two largest charge group radii (0.

RE: [gmx-users] How to obtain the average radial density functions relative to the center of mass with g_rdf.

http://matdl.org/matdlwiki/index.php/softmatter:Radial_Distribution_Func tion That tells you what a rdf is and what the units are. It is a probability function, so your graph is saying that you are 25 times more likely to find the tails 1 nm from the center versus in the bulk. If you wa

[gmx-users] How to obtain the average radial density functions relative to the center of mass with g_rdf.

Dear GMXusers, Last week, i asked a question about the calculation of average radial density functions relative to the center of mass of a micelle formed with DPC molecules (rdf). Unfortunately i received no response. So i re ask my question. So I would like to obtain the average rdf function (in

Re: [gmx-users] H-bond autocorrelation doubts

That's odd, unless the values are -666. I just looked at the source code, and it seems as if the temperature is passed on to the right functions. Erik bipin singh skrev 2011-02-28 19.34: NO, its giving same result no matter what temperature you provide using -temp option. On Mon, Feb 28, 20

Re: [gmx-users] H-bond autocorrelation doubts

NO, its giving same result no matter what temperature you provide using -temp option. On Mon, Feb 28, 2011 at 23:55, Erik Marklund wrote: > It computes the same acf, but the thermodynamic/kinetic calculations give > different results for different -temp, don't they? > > Erik > > bipin singh skr

Re: [gmx-users] H-bond autocorrelation doubts

that temperature has nothing to do with the simulation itself, so the ACF will not change (it is meant for the analysis of Gibbs energy associated with the breaking of that hydrogen bond you are analysing). best Andre On Mon, Feb 28, 2011 at 2:01 PM, bipin singh wrote: > Thanks for your suggest

Re: [gmx-users] Help regarding terinary complex simulation with ZN at active site

kala wrote: Dear friends I am trying to run a MD simulation with a Zn ion in the active site. The zinc makes covalent bond to His , Asp , Cys and Drug molecule. however I am trying to study various ligands that make a sustainable bond with zn over period of time. I am new to

Re: [gmx-users] H-bond autocorrelation doubts

It computes the same acf, but the thermodynamic/kinetic calculations give different results for different -temp, don't they? Erik bipin singh skrev 2011-02-28 18.01: Thanks for your suggestions. Can you please give some explanation for my second doubt... 2011/2/28 André Farias de Moura ma

[gmx-users] Help regarding terinary complex simulation with ZN at active site

Dear friends I am trying to run a MD simulation with a Zn ion in the active site. The zinc makes covalent bond to His , Asp , Cys and Drug molecule. however I am trying to study various ligands that make a sustainable bond with zn over period of time. I am new to gmx and I am prett

Re: [gmx-users] oplsaa galactose

Thanks Justin! Quoting "Justin A. Lemkul" : nishap.pa...@utoronto.ca wrote: Hello, I am trying to simulate hexopyronase using OPLS-AA forcefield using parameters from the paper: An improved OPLS?AA force field for carbohydrates, 2002 by Gunsteren. I was looking through the ffoplsa

Re: [gmx-users] oplsaa galactose

nishap.pa...@utoronto.ca wrote: Hello, I am trying to simulate hexopyronase using OPLS-AA forcefield using parameters from the paper: An improved OPLS?AA force field for carbohydrates, 2002 by Gunsteren. I was looking through the ffoplsaabon.itp file and there are some dihedral parame

[gmx-users] oplsaa galactose

Hello, I am trying to simulate hexopyronase using OPLS-AA forcefield using parameters from the paper: An improved OPLS?AA force field for carbohydrates, 2002 by Gunsteren. I was looking through the ffoplsaabon.itp file and there are some dihedral parameters for hexopyronase. I am not s

Re: [gmx-users] AlF4 - producing LINCS errors

Thanks, that solved it! On 28/02/11 11:24, Mark Abraham wrote: On 02/28/11, *Matthew Cliff * wrote: Hi, I'm very new to MD and I am trying to run MD simulations of proteins binding AlF4-. I am running GROMACS 4.5.3 and using OPLSAA forcefield, Tip4p water. I have created a topology fi

[gmx-users] Re: Regarding without solvent(water).

Please keep all Gromacs-related correspondence on the gmx-users list. I am not a private tutor. ajanihar...@gmail.com wrote: Respected sir, Sir, can I do simulation without water ? I dont want use water as solvent in simulation box. I want do simulation of only protein no any another solve

Re: [gmx-users] question about GBSA and opls-aa

Thank you very much Per! I was quite confused when read the papers (by many things, not only the treatment of the interactions) and now after your explanation, it is never clearer. Thanks a lot! Baoqiang -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/g

Re: [gmx-users] H-bond autocorrelation doubts

Thanks for your suggestions. Can you please give some explanation for my second doubt... 2011/2/28 André Farias de Moura > the manual does not enclose all the necessary knowledge for any kind of MD > simulation or analyses, so you have to read some papers and textbooks as > well.as I've alre

Re: [gmx-users] Regarding without solvent(water).

ajanihar...@gmail.com wrote: Hi everyone, I am using gromacs 4.5.3 version I have query regarding solvent. My protein is completly hydrophobic. So i dont want use a solvent(water). So how to neutralize protein without water. Then what solvent do you intend to use? Can i run grom

Re: [gmx-users] question about GBSA and opls-aa

Hi! The treatment of 1-2, 1-3 and 1-4 interactions with gbsa differ between the different born radii models, but not between force fields. For the Still model, polarisation energies are computed once for 1-2, 1-3 and 1-4 interactions, and never updated for these. For the HCT/OBC models, all in

Re: [gmx-users] H-bond autocorrelation doubts

the manual does not enclose all the necessary knowledge for any kind of MD simulation or analyses, so you have to read some papers and textbooks as well. as I've already pointed out, g_hbond reads the whole set of frames, but the results are meaningful (in the sense of having a homogeneous varianc

[gmx-users] question about GBSA and opls-aa

Hi, I'm using GBSA with opls-aa force field and have some questions that I couldn't find answers, I'd definitely be grateful if could get answer of tips. How does GBSA treat 1-2(covalent bonded), 1-3(bonded angle), 1-4(improper torsion) interactions? Should they all contribute nothing to GBSA ener

[gmx-users] Regarding without solvent(water).

Hi everyone, I am using gromacs 4.5.3 version I have query regarding solvent. My protein is completly hydrophobic. So i dont want use a solvent(water). So how to neutralize protein without water. Then what solvent do you intend to use? Can i run gromacs without water ? Sure, you ca

[gmx-users] H-bond autocorrelation doubts

Hello, I am usng g_hbond to calculate H bond auto correlation during the simulation for two residues in my system, I have two doubts regarding this: 1)How to use -acflen to calculate autocorrelation for all the frames instead of half of the frames 2) What is the use of -temp option in calculating

Re: [gmx-users] Regarding without solvent(water).

ajanihar...@gmail.com wrote: Hi everyone, I am using gromacs 4.3 beta. There is no such version. You probably shouldn't be any sort of beta version for any other purpose but to debug and test new features. I have query regarding solvent. My protein is completly hydrophobic. So i dont

[gmx-users] Regarding without solvent(water).

Hi everyone, I am using gromacs 4.3 beta. I have query regarding solvent. My protein is completly hydrophobic. So i dont want use a solvent(water). So how to neutralize protein without water. Can i run gromacs without water ? my simulation has charged residue in protein. -- gmx-users mail

Re: [gmx-users] .tdr file not created

sakthi kumaran wrote: hi I installed gromacs through the synaptics package manager in ubuntu 10.10 Since I am new to linux. So after installation when I tried to run the example tutorials available in tutor folder, its not running. When I tried to run the program water the .tdr file is no

Re: [gmx-users] about -CN triple bond

On 02/28/11, "C.Y. Chang" wrote: > Hi, > > I try to add a dummy atom in my small molecular pdb and > topology file. (attached files) > But the MDS process still shut down. > The msg. is > [1]+  Exit 255    nohup mdrun -v -deffnm npt_cmplx > > > Could you give me some suggestion

Re: [gmx-users] AlF4 - producing LINCS errors

On 02/28/11, Matthew Cliff wrote: > Hi, > >     I'm very new to MD and I am trying to run MD simulations of proteins > binding AlF4-. I am running GROMACS 4.5.3 > and using OPLSAA forcefield, Tip4p water. > I have created a topology file for AlF4 (see below), and added atom types to > the fo

[gmx-users] AlF4 - producing LINCS errors

Hi, I'm very new to MD and I am trying to run MD simulations of proteins binding AlF4-. I am running GROMACS 4.5.3 and using OPLSAA forcefield, Tip4p water. I have created a topology file for AlF4 (see below), and added atom types to the forcefield files atomtypes and ffnonbonded (see bott