[gmx-users] [Fwd: installing gromacs on vista]

Hi, I am not a free private help service. Please search the GROMACS webpage first, where your question is answered. If you have a specific problem, please ask the mailing list. On point, GROMACS is a simulation package, not a molecule viewer. Mark Original Message

[gmx-users] How can I reconstruct the system in CGMD simulation?

greetings GMX users, When I use genbox command for filling solvent in CGMD simulation with Gromacs suit, I must use a larger van der Waals distance to avoid crashes. when I use default value (0.105nm), system will crash. Which distance is suitable for performing CGMD simulation. I used 0.15 or

Re: [gmx-users] How can I reconstruct the system in CGMD simulation?

rasoul nasiri wrote: greetings GMX users, When I use genbox command for filling solvent in CGMD simulation with Gromacs suit, I must use a larger van der Waals distance to avoid crashes. when I use default value (0.105nm), system will crash. Which distance is suitable for performing CGMD

Re: [gmx-users] How can I reconstruct the system in CGMD simulation?

Hi, My purpose is finding of denaturation mechanism of proteins with MArtini CGFF by Gromacs. I mean after filling box in which there are beads of protein from water beads with suitable van der wall distance (larger than 0.105nm), when I want to start production phase, first switch back to the

Re: [gmx-users] How can I reconstruct the system in CGMD simulation?

I suggest you read the original paper for Martini Protein FF. I think it is not suitable for your purpouse. 2009/12/17 rasoul nasiri nasiri1...@gmail.com Hi, My purpose is finding of denaturation mechanism of proteins with MArtini CGFF by Gromacs. I mean after filling box in which there are

Re: [gmx-users] How can I reconstruct the system in CGMD simulation?

yes, I know there will be limitation for modeling of Folding/Unfolding proteins with MARtini CGFF if I want to look at complete folding/unfolding mechanism of proteins but I want to find out localized regions of the protein (e.g. the C- or N-termini) that they have contribution to the denaturation

[gmx-users] the resource of Vdw Radii in Vdwradii.dat

Hi all I am a new in using Gromacs 4 I now using g_sas to calculate the solvent accessible surface. Yet, the outcome informs me the Vdw radius is missing for P atom in Vdwradii.dat. Thus I check the file and want to add the value for P. However, though I read through the Manual, I can not

Re: [gmx-users] How can I reconstruct the system in CGMD simulation?

rasoul nasiri wrote: yes, I know there will be limitation for modeling of Folding/Unfolding proteins with MARtini CGFF if I want to look at complete folding/unfolding mechanism of proteins but I want to find out localized regions of the protein (e.g. the C- or N-termini) that they have

Re: [gmx-users] the resource of Vdw Radii in Vdwradii.dat

On 12/17/09 5:43 PM, huikuan chao wrote: Hi all I am a new in using Gromacs 4 I now using g_sas to calculate the solvent accessible surface. Yet, the outcome informs me the Vdw radius is missing for P atom in Vdwradii.dat. Thus I check the file and want to add the value for P. However,

[gmx-users] How is calculated the bind free energy GROMACS???

Hi, I need to know how to calculated GROMACS, the bind free energy, words, equations used to calculated the bind free energy in the sub-program g_lie. Thank you Deisy Y. Rodriguez S. Practicante de Computos Avanzados Grupo de Investigacion en Fisicoquimica Teorica y Experimental GIFTEX

[gmx-users] Re: gmx-users Digest, Vol 68, Issue 86

Hi All: I just wanted to add my 2 cents to the already excellent comments posted about the conversion of different types of ion Lennard-Jones parameters, since I get lots of emails about this very subject. It is misleading to think of an ion parameter as a SINGLE value of sigma and epsilon. The

[gmx-users] Re: sulfate atomtype for ffgmx (Justin A. Lemkul)

Thank you both for the suggestions. My system does also contain carbohydrates (sugar) and ffoplsaa.atp does not contain the atomtypes for these molecules. Even though carbohydrate parameters have been published for OPLS they are not present in the ffoplsaa.atp file. I did look into the

[gmx-users] error with changing pdb file

Hello, While I am simulating my simulations, I encountered below error. I have pdb file which is: HEADERPROTEINTITLE (5,5) Nanotube (1,1,80) replicationAUTHORTubeGen 3.3, J T Frey, University of DelawareEXPDTATHEORETICAL MODELATOM 1 C UNK 1 3.410 0.000

Re: [gmx-users] error with changing pdb file

ksm tprk wrote: Hello, While I am simulating my simulations, I encountered below error. I have pdb file which is: HEADERPROTEIN TITLE (5,5) Nanotube (1,1,80) replication AUTHORTubeGen 3.3, J T Frey, University of Delaware EXPDTATHEORETICAL MODEL ATOM 1 C UNK 1

[gmx-users] LIE precision and accuracy

Hello,   I am in the middle of using Gromacs 3.3.3 to evaulate interaction energies between a protein and two separate ligands to compare their binding affinities. In doing this I have run each solvated complex through a 1 ns MD simulation and each solvated ligand through a 1 ns MD

Re: [gmx-users] error with changing pdb file

ksm tprk wrote: I changed pdb file after that I generated topology file. It appears you are relying on grompp to figure out what parameters should be used for these angles, and apparently, given these atom types, there are no default values available in the force field you've chosen to

Re: [gmx-users] LIE precision and accuracy

On 12/17/09 9:24 PM, Marc Charendoff wrote: Hello, I am in the middle of using Gromacs 3.3.3 to evaulate interaction energies between a protein and two separate ligands to compare their binding affinities. In doing this I have run each solvated complex through a 1 ns MD simulation and

[gmx-users] LIE precision and accuracy

In spite of the fact that I have never used g_lie, I have used a variety of different techniques to calculate binding free energies, and I would be astounded if it was possible to get the precision that you desire with only 1 ns of sampling per state. Are you sure that the reported

Re: [gmx-users] error with changing pdb file

ksm tprk wrote: Hello Justin, I looked at in my gromacs/3.3.1 and it ahs only ffgmx.n2t force field file. because of that, I chaged to new version gromacs. I tried to use different force filed but new version gromacs but they didn't work. I used gromacs/4.0.5 and I created .gro and by

[gmx-users] trjcat error

Hi ALL, I have 3 5 nano-seconds trajectory files (.trr) of a protein+lipid+water simulation. I am using trjcat to join them into a single .trr file for analysis and getting the following error:

Re: [gmx-users] trjcat error

Hi Anirban, Check each trajectory with gmxcheck to see whether they are okay. Cheers, Tsjerk On Fri, Dec 18, 2009 at 7:32 AM, Anirban Ghosh reach.anirban.gh...@gmail.com wrote: Hi ALL, I have 3 5 nano-seconds trajectory files (.trr) of a protein+lipid+water simulation. I am using trjcat to