[gmx-users] RE: how many water molecule used to run MD?

> If I want to include more than 1000 TIP4P or TIP5P water molecules in > my MD system, how could I construct the TIP4P.gro and TIP5P.gro files > ? genconf -f onewater.gro -o box.gro -nbox N N N, where onewater.gro contains the coordinates of one water molecule and N - is a number of water molecu

[gmx-users] RE: how many water molecule used to run MD?

> Hi > how many water molecules used to run MD? > > what is the criteria for this? So many to make your short-range potential saturated. -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban tel.: +

[gmx-users] RE: TIP4P and TIP5P

> Could anyone tell me how to construct the solvent box of TIP4P and TIP5P > model? First of all you should make the coordinates of one particle of the desired model in .gro file format. For the next commands see my previous messages. Cheers. -- Vitaly V. Chaban School of Chemistry National

[gmx-users] Re: how many water molecule used to run MD?

Hi Would you please explain "the short-range potential saturated"? What is the short-range potential? Also, how to measure the short-range potential? Thank you Lin On 9/22/08, Vitaly Chaban <[EMAIL PROTECTED]> wrote: > > Hi > > how many water molecules used to run MD? > > > > what is the crit

[gmx-users] Atom type: N inside the R-N(CH3)3

Hi What is the atom type of Nitrogen inside the molecule R-N(CH3)3 ? I check the ffG53a5.itp and ffG53a6.itp and the related Gromos FF papers. There are 6 atom types for Nitrogen. N peptide nitrogen (NH) NT terminal nitrogen (NH2) NL terminal nitrogen (NH3) NR aromatic

RE: [gmx-users] PME 3dc geometry and the optimal PME mesh load

Yes. The manual and also mdp options of the jsut released 4.0 version will tell you that you can increase your cut-off and PME grid spacing by the same factor to lower the PME load. Berk Date: Sun, 21 Sep 2008 23:24:13 +0800 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: [gmx-user

[gmx-users] Re[2]: how many water molecule used to run MD?

CYL> Would you please explain "the short-range potential saturated"? Usually it is the same as Lennard-Jones potential. The each side of your box must be two times larger (see also about cut-off) than the distance where the value of the short-range potential is (very close to) zero. In fluids, th

Re: [gmx-users] Leaflet of Bilayer

(Yes, what Chris Neale said).  I had to do something similar myself, to make a 256-lipid square box from a 128 lipid box.  I used genbox to make a new, larger square box using my original lipid patch as the input file, and then tinkered with the dimensions to get the lipids/leaflet as close to w

Re: [gmx-users] TIP4P and TIP5P

You don't have to construct that stuff. Its all in the share/gromacs/top directory of your gromacs installation. Check the gro and the itp files there. Jochen Chih-Ying Lin wrote: > Hi > Could anyone tell me how to construct the solvent box of TIP4P and TIP5P > model? > > > And, how to cons

Re: [gmx-users] Cann't get the same result ?

xuji wrote: > Hi all: > > I run mdrun of gromacs-3.3.3 6 times of a small simulation, > but I cann't get the same result every time. I run the mdrun > program using "./mdrun -v -s md1.tpr -o md1.trr -c after_md1.gro -g > md1.log -e md1.edr -x md1.xtc > md1.job >&& ./mdrun -v -s md1.tp

Re: [gmx-users] output format of gromacs utilities

Vitaly Chaban wrote: > Hello, > > In gromacs analysis tools, is it possible to output multiple data > columns as several 'parallel' columns (not as pairs delimited by '&')? I don't think so, but i once wrote a script that does the transformation for you. Here it is. Best, Jochen #!/bin/bash t

RE: [gmx-users] output format of gromacs utilities

Hi, For many tools setting the environment variable GMX_VIEW_XVG = xmgr will work. Berk > Date: Mon, 22 Sep 2008 11:05:58 +0200 > From: [EMAIL PROTECTED] > To: [EMAIL PROTECTED]; gmx-users@gromacs.org > Subject: Re: [gmx-users] output format of gromacs utilities > CC: > > Vitaly Chaban wrote:

[gmx-users] searching the archives

Shalom, Is it just me or there is a bug in the archives search page http://www.gromacs.org/search ? (error 404 - page not found) --omer. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search th

Re: [gmx-users] searching the archives

Omer Markovitch wrote: Shalom, Is it just me or there is a bug in the archives search page http://www.gromacs.org/search ? (error 404 - page not found) --omer. plz go to the main site and click search. __

Re[2]: [gmx-users] output format of gromacs utilities

Jochen, Thank you very much! I will just try it. Vitaly JH> Vitaly Chaban wrote: >> Hello, >> >> In gromacs analysis tools, is it possible to output multiple data >> columns as several 'parallel' columns (not as pairs delimited by '&')? JH> I don't think so, but i once wrote a script that doe

[gmx-users] simulation in DPPC lipid bilayer

Dear Users I am trying to do a simulation in lipid using DPPC12a.pdb.I have done all the necessary changes rewuired.I am using FFGMX force field while doing positional restarined step its giving following error: Range checking error: Explanation: During neighborsearching, we assign each particle

Re: [gmx-users] simulation in DPPC lipid bilayer

prasun kumar wrote: Dear Users I am trying to do a simulation in lipid using DPPC12a.pdb.I have done all the necessary changes rewuired.I am using FFGMX force field while doing positional restarined step its giving following error: Range checking error: Explanation: During neighborsearching

[gmx-users] Re:Leaflet of Bilayer

Thanks alot to Chris and Alan for given their valuable suggestions then a small doubt about time length of bilayer simulation, that is if I concentrate mainly on protein but not on membrane is it require to run >=50ns or 20ns of POPC alone before inserting protein into it. Earlier I performe

[gmx-users] Polystyrene box

Hello, we are trying to generate a polystyrene box. We have a homemade pdb file, but the residues are not recognised. Have somebody a good pdb file or can tell me what are the standard residues in Gromax? Any other good hints are welcome. Thanks a lot, Andrea _

[gmx-users] MD for two merged chains

Hello, I have a two-chain protein. I want to merge N-terminal residue of chain A with C-terminal of chain B. I can tweak the coordinates with pymol but when I run energy minimization two chains split again because gromacs fairly treats the input as a two-chain protein. I could switch the ATOM ent

Re: [gmx-users] Announcing: Gromacs 4.0, release candidate 1

What compiler should I use on Windows? Thank you in advance. --- On Sun, 9/21/08, Erik Lindahl <[EMAIL PROTECTED]> wrote: From: Erik Lindahl <[EMAIL PROTECTED]> Subject: [gmx-users] Announcing: Gromacs 4.0, release candidate 1 To: "Discussion list for GROMACS users" Date: Sunday, September 21, 2

Re: [gmx-users] Announcing: Gromacs 4.0, release candidate 1

Hi, One extra comment: By default, checkpointing will result in separate output files to avoid filling up your disk, or just in case something horrible happens just when we are about to resume the simulation. There are also some old strange versions of the GPFS file system where append o

Re: [gmx-users] Announcing: Gromacs 4.0, release candidate 1

MSVC should be able to compile it, but you'll have to create the makefiles/build environment yourself. Alternatively, the easy route is to install cygwin (or get a mac ;-) Cheers, Erik On Sep 22, 2008, at 4:36 PM, Sagittarius wrote: What compiler should I use on Windows? Thank you in advan

Re: [gmx-users] Polystyrene box

Andrea Muntean wrote: Hello, we are trying to generate a polystyrene box. We have a homemade pdb file, but the residues are not recognised. Have somebody a good pdb file or can tell me what are the standard residues in Gromax? Any other good hints are welcome. Residues that are recognize

[gmx-users] Search more information of Atom type: N inside the R-N(CH3)3

Hi What is the atom type of Nitrogen inside the molecule R-N(CH3)3 ? I check the ffG53a5.itp and ffG53a6.itp and the related Gromos FF papers. There are 6 atom types for Nitrogen. N peptide nitrogen (NH) NT terminal nitrogen (NH2) NL terminal nitrogen (NH3) NR aromatic

Re: [gmx-users] Announcing: Gromacs 4.0, release candidate 1

Erik Lindahl wrote: MSVC should be able to compile it, but you'll have to create the makefiles/build environment yourself. Alternatively, the easy route is to install cygwin (or get a mac ;-) or keep your computer and run it under Linux :D (I can not resist) Nuno Azoia Cheers, Erik On Sep

Re: [gmx-users] Search more information of Atom type: N inside the R-N(CH3)3

Chih-Ying Lin wrote: Hi What is the atom type of Nitrogen inside the molecule R-N(CH3)3 ? I check the ffG53a5.itp and ffG53a6.itp and the related Gromos FF papers. There are 6 atom types for Nitrogen. N peptide nitrogen (NH) NT terminal nitrogen (NH2) NL terminal nitroge

[gmx-users] Calculating Temperature from Velocity

I am trying to calculate the temperature from the final velocity posted in the confout.gro file after a simulation runs. I have implemented a berendsen thermostat to control the temperature to 300K and ran it for 1ns. Looking at g_energy the final temperature of the system is 299.981. Statistics ov

[gmx-users] #include "ffXXX.itp"

Hi The command #include "ffXXX.itp" is putting in the .top file. I was told that this command will automatically assign the force field parameters which I did not assign in my .top file. I want to print out the complete force field paramters which the command "#include "ffXXX.itp" assigned. Woul

Re: [gmx-users] #include "ffXXX.itp"

Chih-Ying Lin wrote: Hi The command #include "ffXXX.itp" is putting in the .top file. I was told that this command will automatically assign the force field parameters which I did not assign in my .top file. I want to print out the complete force field paramters which the command "#include "f

[gmx-users] RE: Announcing: Gromacs 4.0, release candidate 1

> What compiler should I use on Windows? > Thank you in advance. If you succeed it would be great if you share the resulting binaries in the internet! -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvc

Re: [gmx-users] Calculating Temperature from Velocity

Andy Shelley wrote: > I am trying to calculate the temperature from the final velocity posted in > the confout.gro file after a simulation runs. I have implemented a berendsen > thermostat to control the temperature to 300K and ran it for 1ns. Looking at > g_energy the final temperature of the syst

[gmx-users] RE: #include "ffXXX.itp"

> I want to print out the complete force field paramters which the command > "#include "ffXXX.itp" assigned. Goto /usr/local/gromacs/share/gromacs/top/ on your system. If the parameters mentioned in ffXXX.itp are redefined in your .top you get a warning by grompp. -- Vitaly V. Chaban School of

[gmx-users] tpbconv*

Hi users, I am running membrane protein simulation in between system crashed due to power fluctuations, I am trying to extend this run by using tpbconv command tpbconv -f 1ns.trr -e 1ns.edr -s 1ns.tpr -o new1ns.tpr it showed that Reading toplogy and shit from 1ns_2timeTh6_9inpopc.tpr Reading file

[gmx-users] #include "ffXXX.itp"

HI The command #include "ffXXX.itp" is putting in the .top file. How does this command automatically assign the force field parameters which I did not assign in my .top file? Is it based on the atom types which I assign in my .top file? Then, all the force field parameters from "include ff

[gmx-users] Re: #include "ffXXX.itp"

Chih-Ying Lin wrote: HI The command #include "ffXXX.itp" is putting in the .top file. How does this command automatically assign the force field parameters which I did not assign in my .top file? Is it based on the atom types which I assign in my .top file? Then, all the force field pa

Re: [gmx-users] tpbconv*

sudheer babu wrote: Hi users, I am running membrane protein simulation in between system crashed due to power fluctuations, I am trying to extend this run by using tpbconv command tpbconv -f 1ns.trr -e 1ns.edr -s 1ns.tpr -o new1ns.tpr it showed that Reading toplogy and shit from 1ns_2timeTh

[gmx-users] Forming a micelles

Hi I heard that it takes very long to see a micelle forming. How long should be the simulation time to see the micelle forming? How many nanoseconds to put on the simulation? Is there any particular difference to simulate the micelles than other system? My simulation steps are 1. prepare the topo

[gmx-users] Re: Calculating Temperature from Velocity

A few more questions added to my first response. When calculating the Temperature should I use the mass of the molecule or of the atoms times the velocity of the atoms or velocity of the molecule? Also, when looking at the output of g_traj if I create a small group of atoms close to each other, sa

[gmx-users] RE: #include "ffXXX.itp"

> How does this command automatically assign the force field > parameters which I did not assign in my .top file? It inserts the content of ffXXX.itp into .top file. -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROT

[gmx-users] Re: #include "ffXXX.itp"

Hi >From Justin: " Yes, as long as those atoms are listed as bonded within the [ bonds ] section of your .top file. " The specific "bonded function", such as gb_28", should be also listed on the [bonds] section, right? Or, it could assign NOTHING for me, right? so, [bonds] ; ai aj funct 8

[gmx-users] Re: Calculating Temperature from Velocity

Hi Andy, > I create a small group of atoms close to each other, say > 10-12 atoms, the temperature of these atoms varies alot while the > temperature the whole system does not, why is this? A mob is always uniform. :) You have a normal situation indeed. > Is there a way to > accurately determin

[gmx-users] RE: Forming a micelles

> I heard that it takes very long to see a micelle forming. I believe it's quite true. > How long should be the simulation time to see the micelle forming? > How many nanoseconds to put on the simulation? I suggest you to use ngmx (or VMD) to monitor the trajectory and catch the moment you are i

[gmx-users] The box size and the # of the solute / water molecules?

Hi What size of the simulation system can be really represent the real situation? Once I decide the box size, the water density can determine the # of water molecules to put in. And, the concentration can determine the # of the solute to put in. Is the procedure correct? Thank you Lin __

[gmx-users] Re: #include "ffXXX.itp"

Chih-Ying Lin wrote: so, [bonds] ; ai aj funct 8 9 gb_28 is correct... No. The function type is not the same as a bond type. Read in Chapter 5 about the difference. If you have atoms 8 and 9 as a bond, with the appropriate function type, the grompp will assign the values

[gmx-users] Two independent umbrellas in gromacs 3.3.1

Here are some source code modifications that allow two reference groups for the pull code (umbrella option). It would be simple to mod this for more than two groups. It would be slightly more difficult to enable all pull options (e.g. constraints) with more than one reference group, as that

Re: [gmx-users] Forming a micelles

Chih-Ying Lin wrote: Hi I heard that it takes very long to see a micelle forming. How long should be the simulation time to see the micelle forming? How many nanoseconds to put on the simulation? Is there any particular difference to simulate the micelles than other system? My simulation steps

Re: [gmx-users] tpbconv*

sudheer babu wrote: > Hi users, > I am running membrane protein simulation in between system crashed due to > power fluctuations, I am trying to extend this run by using tpbconv command > tpbconv -f 1ns.trr -e 1ns.edr -s 1ns.tpr -o new1ns.tpr > it showed that > > Reading toplogy and shit from 1ns_