Re: [gmx-users] Inserting protein in Bilayer

sunny mishra wrote: Hi Justin, I have successfully created the lipid bilayer and inserted the protein inside that but now I feel that before doing all that I would have placed the water molecules or lipid molecules at some specific point. Some "specific point" in your workflow? Or the simulati

Re: [gmx-users] Advantage of NPT over NVT?

Pan Wu wrote: Hello everyone, Is there any advantage of using NPT ensemble over NVT? Sure. Most experimental data is measured from NPT. If using REMD, you avoid non-physical pressures at high temperature. Seems people doing simulation with gromacs like to use NPT (for protein + solvent

Re: [gmx-users] g_hbond and fluor

David van der Spoel wrote: > Alvaro Cortes wrote: >> Hi all. >> >> I'm new at the list so i don't know if something similar has been >> discussed before. >> I tried to search in the archives, but i can't find something similar. >> >> I have a doubt about g_hbond and fluor acceptors. As i can see in

Re: [gmx-users] Advantage of NPT over NVT?

Hi, The simplest ensemble is NVE. Historically, NVT came later to allow simulations in constant temperature which seem to be more realistic from an experimental point of view. However, experiments are usually performed under constant pressure and temperature, which is the reason for people to choo

[gmx-users] protein domain separate

Hi I want to do MD on a two-domain protein (Protein A, Protein B). After doning position restranit for 20 ps, the final structure separated. How could I keep these 2 domain close to each other during whole MD run. Thank you in advance. -- Tehran University of Medical Sciences www.tums.ac.ir

Re: [gmx-users] Advantage of NPT over NVT?

Hi, In addition to the remarks of Ran and Mark, also note that with NVT the density of your system may change significantly and artificially, relating to changes in your protein. This in turn affects the dynamics of your protein, which should be considered an artefact of NVT simulations. Cheers,

[gmx-users] Opening aminoacids.dat file during grommp

Hello all, I am running grommp which kind of goes "successfully" but I am a little concerned about the fact that one of the messages in the terminal says "opening aminoacids.dat file" and in another message says "OTHER: 2000 residues found." I guess this 2000 is refering to the 2000 water molecul

Re: [gmx-users] eliminating forces on certain direction

Hi Mark, Haha. Yes, your words is right. My objective is to study the interaction between ions and walls. I think the ions may be attached in the wall so the velocity getten from MD simulation is always bigger than the continuum theory's prediction. So I want to build a simulation on which ion can

Re: [gmx-users] protein domain separate

hazizian wrote: Hi I want to do MD on a two-domain protein (Protein A, Protein B). After doning position restranit for 20 ps, the final structure separated. How could I keep these 2 domain close to each other during whole MD run. Check that they're not separated because of a PBC artefact (try

Re: [gmx-users] Opening aminoacids.dat file during grommp

Lum Nforbi wrote: Hello all, I am running grommp which kind of goes "successfully" but I am a little concerned about the fact that one of the messages in the terminal says "opening aminoacids.dat file" and in another message says "OTHER: 2000 residues found." I guess this 2000 is refering to

Re: [gmx-users] eliminating forces on certain direction

吴鹏 wrote: Hi Mark, Haha. Yes, your words is right. My objective is to study the interaction between ions and walls. I think the ions may be attached in the wall so the velocity getten from MD simulation is always bigger than the continuum theory's prediction. So I want to build a simulation o

[gmx-users] grompp output on terminal

Hello everyone, I had written earlier today about my concern involving grompp. I am trying to minimize the energy of a pure water system using grompp: grompp -f waters.mdp -c waters_b.gro -p water.top -o watersinput.tpr and part of the output on the terminal is as follows: Analysing resid

[gmx-users] Is there something wrong with the Gromacs site?

I'm getting: Site settings could not be loaded We were unable to locate the API to request site settings. Please see below for debugging information. HTTP Response Status Code: 500 The API says: wiki 'www.gromacs.org' has failed to initialize or did not start up properly: Initialization excepti

Re: [gmx-users] Is there something wrong with the Gromacs site?

ditto. I hope they are upgrading the server. On Tue, Oct 13, 2009 at 11:29 AM, Michael Shirts wrote: > I'm getting: > > Site settings could not be loaded > > We were unable to locate the API to request site settings. Please see > below for debugging information. > > HTTP Response Status Code: 50

[gmx-users] What is best way to get multiple chains?

Hi, I am a gmx newbie, so please don't bite too much! :) Learning gmx, I am experimenting with simulations with multiple identical small chains. What I did was: - I generated the peptides with pymol - Generated a .gro with pdb2gmx - Used editconf to create translated copies - Stitching them toge

Re: [gmx-users] eliminating forces on certain direction

Hi Mark, What you said reminds me to think deeply about my speculation. Thanks for your remind and I hope to discuss it with you when I get some ideas on that. Peng Wu On Tue, Oct 13, 2009 at 10:02 AM, Mark Abraham wrote: > 吴鹏 wrote: > >> Hi Mark, >> >> Haha. Yes, your words is right. My object

Re: [gmx-users] grompp output on terminal

Lum Nforbi wrote: Hello everyone, I had written earlier today about my concern involving grompp. I am trying to minimize the energy of a pure water system using grompp: grompp -f waters.mdp -c waters_b.gro -p water.top -o watersinput.tpr and part of the output on the terminal is as follow

Re: [gmx-users] Advantage of NPT over NVT?

Pan Wu wrote: Hello everyone, Is there any advantage of using NPT ensemble over NVT? Seems people doing simulation with gromacs like to use NPT (for protein + solvent system). However, for NPT, there is one parameter "compressibility" which is tricky to choose; for NVT, it is so simple.

Re: [gmx-users] Advantage of NPT over NVT?

The experimental value of the compressibility of n-alkanes, DMS, and 1-alcohols can be found in following reference document. http://www.rsc.org/publishing/journals/CP/article.asp?doi=b206425a On Tue, Oct 13, 2009 at 4:08 PM, Justin A. Lemkul wrote: > > > Pan Wu wrote: > >> Hello everyone, >>

Re: [gmx-users] Inserting protein in Bilayer

sunny mishra wrote: Hi Justin, I have successfully created the lipid bilayer and inserted the protein inside that but now I feel that before doing all that I would have placed the water molecules or lipid molecules at some specific point. I want to create a lipid bilayer in which protein is in

Re: [gmx-users] What is best way to get multiple chains?

ms wrote: Hi, I am a gmx newbie, so please don't bite too much! :) Learning gmx, I am experimenting with simulations with multiple identical small chains. What I did was: - I generated the peptides with pymol - Generated a .gro with pdb2gmx - Used editconf to create translated copies - Stitc

[gmx-users] Check out my photos on Facebook

Hi gmx-users@gromacs.org, I set up a Facebook profile where I can post my pictures, videos and events and I want to add you as a friend so you can see it. First, you need to join Facebook! Once you join, you can also create your own profile. Thanks, Mohit To sign up for Facebook, follow the li

[gmx-users] RMSF reference state?

Hi everyone,Thank you for answering my former questions, it really help me, the new gmx-er a lot~ Here is another question about reference state of RMSF. In the manual, it shows "g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard deviation) of atomic positions after (

Re: [gmx-users] RMSF reference state?

Pan Wu wrote: Hi everyone, Thank you for answering my former questions, it really help me, the new gmx-er a lot~ Here is another question about reference state of RMSF. In the manual, it shows "g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard deviation) of at

[gmx-users] major issue with gmx-4.0.3?

Dears, I recall the report of a major issue in gmx-4.0.3. At the time this made me put gmx403 on the side of "not to be used versions". I can not find a trace of it ... anyone would remember anything? Thanks, XAvier. ___ gmx-users mailing listgm

Re: [gmx-users] major issue with gmx-4.0.3?

XAvier Periole wrote: Dears, I recall the report of a major issue in gmx-4.0.3. At the time this made me put gmx403 on the side of "not to be used versions". I can not find a trace of it ... anyone would remember anything? I thought the major problem was with 4.0.1 - it had something broke

Re: [gmx-users] What is best way to get multiple chains?

ms wrote: Hi, I am a gmx newbie, so please don't bite too much! :) Learning gmx, I am experimenting with simulations with multiple identical small chains. What I did was: - I generated the peptides with pymol - Generated a .gro with pdb2gmx This step is "generating a molecular topology". You

[gmx-users] run g_cover in parallel

Hi, I wonder if there a way to run g_cover in paralel in order to make things run faster? Also, what analysis programs can run in parallel? Best, Itamar --- "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut ==

Re: [gmx-users] run g_cover in parallel

Itamar Kass wrote: Hi, I wonder if there a way to run g_cover in paralel in order to make things run faster? No. Obviously you can use -dt to reduce the number of frames you analyze. Also, what analysis programs can run in parallel? None in 4.0.x. Not sure about future plans. Matk ___

[gmx-users] p0_4238: p4_error: interrupt SIGSEGV: 11

Hello, I am trying to equilibrate glucose in water using Gromacs 4.0.5 version. I am geting the error immidiately after the mdrun starts Warning: 1-4 interaction between 1 and 18 at distance 3.462 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation Th

Re: [gmx-users] p0_4238: p4_error: interrupt SIGSEGV: 11

Nilesh Dhumal wrote: Hello, I am trying to equilibrate glucose in water using Gromacs 4.0.5 version. I am geting the error immidiately after the mdrun starts Warning: 1-4 interaction between 1 and 18 at distance 3.462 which is larger than the 1-4 table size 2.400 nm These are ignored for the re

Re: [gmx-users] p0_4238: p4_error: interrupt SIGSEGV: 11

Nilesh Dhumal wrote: Hello, I am trying to equilibrate glucose in water using Gromacs 4.0.5 version. I am geting the error immidiately after the mdrun starts Warning: 1-4 interaction between 1 and 18 at distance 3.462 which is larger than the 1-4 table size 2.400 nm These are ignored for the

Re: [gmx-users] run g_cover in parallel

Hi, This is strange, 'cause on the site under installing (using MPI) it is written "*In GROMACS 4.x, some of the utility programs are also MPI-aware, but these will only be for compute-intensive utilities (e.g. that diagonalize large matrices, or calculate autocorrelations, etc.).*". So I guess th

[gmx-users] Re: Reg: GROMACS Queries

Please keep all GROMACS-related correspondence on the gmx-users list. I do not advertise myself as a private tutor, nor do I claim to have all the answers. You stand a much better chance of getting useful information by posting to the list. The concept of pH in a simulation is a difficult on

Re: [gmx-users] p0_4238: p4_error: interrupt SIGSEGV: 11

I think your box is too small. try changing them. On Tue, Oct 13, 2009 at 8:05 PM, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> Hello, >> >> I am trying to equilibrate glucose in water using Gromacs >> 4.0.5 version. I am geting the error immidiately after the mdrun starts >> Warning

Re: [gmx-users] p0_4238: p4_error: interrupt SIGSEGV: 11

Yongchul Chung wrote: I think your box is too small. try changing them. What leads you to this conclusion? We have no information about the box. Presumably, the only box that is "too small" would be one that doesn't satisfy the minimum image convention, but grompp fails with a fatal error

[gmx-users] interpolation for tabulated potential

Hello, I'm just wondering what interpolation method is used for the tabulated potential function in GMX. Since GMX 4, the input table contains potential and force, unlike potential and second derivative in GMX 3. Is cubic spline still used in GMX 4? If yes, what algorithm is implemented to get

Re: [gmx-users] run g_cover in parallel

Itamar Kass wrote: Hi, This is strange, 'cause on the site under installing (using MPI) it is written "/In GROMACS 4.x, some of the utility programs are also MPI-aware, but these will only be for compute-intensive utilities (e.g. that diagonalize large matrices, or calculate autocorrelations,

Re: [gmx-users] interpolation for tabulated potential

LuLanyuan wrote: > Hello, > I'm just wondering what interpolation method is used for the tabulated > potential function in GMX. Since GMX 4, the input table contains > potential and force, unlike potential and second derivative in GMX 3. Is > cubic spline still used in GMX 4? If yes, what algori

RE: [gmx-users] interpolation for tabulated potential

I saw it. Thanks. Lanyuan > Date: Wed, 14 Oct 2009 14:50:02 +1100 > From: mark.abra...@anu.edu.au > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] interpolation for tabulated potential > > LuLanyuan wrote: > > Hello, > > I'm just wondering what interpolation method is used for the tabulate

Re: [gmx-users] p0_4238: p4_error: interrupt SIGSEGV: 11

I jumped to the conclusion too fast. Thanks Justin for correcting me. Disregard my previous comment please. On Tue, Oct 13, 2009 at 10:35 PM, Justin A. Lemkul wrote: > > > Yongchul Chung wrote: > >> I think your box is too small. try changing them. >> >> > What leads you to this conclusion? We

[gmx-users] forcefield

Hi, I want to do simulation with the ligand called zebularine. I dont find forcefied for that. Also i read prodgr has been deprecated.. Could you please help me to find out the forcefield for the ligand zebularine. Thanks in advance lalitha __

Re: [gmx-users] major issue with gmx-4.0.3?

I had a look at the notes ... nothing there to satisfy my concerns :)) If gmx-403 is fine on the basic MD level it is then good news. If anybody recalls some thing I would appreciate to be informed. Best, XAvier. XAvier Periole wrote: Dears, I recall the report of a major issue in gmx-4.0.3