[gmx-users] How can I increase maximum number of pulling step for energy minimization?

Hi gromacs users: I use gromacs 4.5.6 for energy minimization with steepest descent method for ubiquitin pulling simulation with pulling step for applying displacement. For that simulation, I should repeat pulling and minimization process. I need 10^4 pulling step calculation to get fully

Re: [gmx-users] How can I increase maximum number of pulling step for energy minimization?

On 10/28/13 1:59 PM, Gwonchan Yoon wrote: Hi gromacs users: I use gromacs 4.5.6 for energy minimization with steepest descent method for ubiquitin pulling simulation with pulling step for applying displacement. For that simulation, I should repeat pulling and minimization process. I need 10^4

Re: [gmx-users] how can I make statics for Z-axis?

g_traj -nox -noy if I recall correctly. On Jan 21, 2013, at 4:10 PM, Albert wrote: hello: I would like to make statics for an atom along Z-axis. I am just wondering how can I to do this in Gromacs? thank you very much best Albert -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] how can I make statics for Z-axis?

HI Erik: thanks a lot for kind advices, I will try it. best Albert On 01/24/2013 03:00 PM, Erik Marklund wrote: g_traj -nox -noy if I recall correctly. On Jan 21, 2013, at 4:10 PM, Albert wrote: hello: I would like to make statics for an atom along Z-axis. I am just wondering how can I

[gmx-users] how can I make statics for Z-axis?

hello: I would like to make statics for an atom along Z-axis. I am just wondering how can I to do this in Gromacs? thank you very much best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at

Re: [gmx-users] how can I create gromos and top file for graphene

On 10/15/12 5:53 PM, Yihua Zhou wrote: Dear Sir/Madam I am trying to use GROMACS to simulate DNA translocation through graphene nanopore, however, I don’t know how to create the *.top and *.gro files for my case, I know I can use pdb2gmx to obtain topology and gromos file for DNA, but I don’t

[gmx-users] How can i specify a user defined potential between i, i+2 residues

Hi all, I use a user defined potential to describe non-bonded interactions, as this excludes i, i+2,i+3. If i want to describe a user defined potential for i,i+2,i+3,(i.e, 1-2,1-3) residues , how can i give that in mdp file. T -- gmx-users mailing list

Re: [gmx-users] How can i specify a user defined potential between i, i+2 residues

On 16/05/2012 3:43 PM, mohan maruthi sena wrote: Hi all, I use a user defined potential to describe non-bonded interactions, as this excludes i, i+2,i+3. If i want to describe a user defined potential for i,i+2,i+3,(i.e, 1-2,1-3) residues , how can i give that in mdp file. Doing

Re: [gmx-users] How can I install Gromacs on Window XP?

On 14/04/2012 11:34 PM, Abhishek Tyagi wrote: Sir, Please provide the appropriate easy way to understand for the installation of gromacs on windows XP. I am not understanding the methodology provided in the installation guide for windows. Please do not address general GROMACS questions to my

[gmx-users] how can i merge several trajectory files to one?

Dear Experts, I am wondering it is possible to merge several trajectory pieces to one ? If it is, how can I ? Best, Hyun. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] how can i merge several trajectory files to one?

Hyunsik wrote: Dear Experts, I am wondering it is possible to merge several trajectory pieces to one ? trjcat -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech

RE: [gmx-users] how can i merge several trajectory files to one?

Thank you very much. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Thursday, December 01, 2011 11:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] how can i merge several trajectory

[gmx-users] how can I get the .top file??

Dear members of gromacs Let you know that I'm a beginner of Gromacs. I am trying to simulate the diffusion problem on some zeolite structure. (especially ZSM-22) From the manual, I knew that the three files are required to get the .tpr input file. I got the .pdb file of my concerned

Re: [gmx-users] how can I get the .top file??

Kiwoong Kim wrote: Dear members of gromacs Let you know that I'm a beginner of Gromacs. I am trying to simulate the diffusion problem on some zeolite structure. (especially ZSM-22) From the manual, I knew that the three files are required to get the .tpr input file. I got the .pdb file

[gmx-users] How can I convert Gromacs ouput to Desmond input file??

Dear experts, Hi, I used to gromacs for MD, but there is need to make desmond file from gromacs output. If there is anyone who know how to this, please let me know. Thank you very much. -Hyun--- gmx-users mailing list

Re: [gmx-users] How can I convert Gromacs ouput to Desmond input file??

On 27/03/11, 김현식 namm...@hotmail.com wrote: !-- .hmmessage P { margin:0px; padding:0px } body.hmmessage { font-size: 9pt; font-family:굴림 } -- Dear experts,   Hi, I used to gromacs for MD, but there is need to make desmond file from gromacs output.

[gmx-users] How can I ...?

Dear All I want to generate .top and .gro files for protein-ligand complex. there are many problems,can every body guide me? Actually it is my M.sc thesis and it has taken much time of me. problems: 1-after using PRODRG server the vector boxes for are not the same 2-ligand's coordinates change

Re: [gmx-users] How can I ...?

On 25/12/2010 11:21 PM, mohsen ramezanpour wrote: Dear All I want to generate .top and .gro files for protein-ligand complex. there are many problems,can every body guide me? Actually it is my M.sc thesis and it has taken much time of me. Yep, research is difficult and time-consuming and hard

[gmx-users] How can I best setup the nodes number

Hi, Estimate for the relative computational load of the PME mesh part: 0.33 How do I set how many nodes I should use? #PBS -l nodes=12:ppn=4 What if the PME mesh part has different values? is it okay? Before I did those kind of very blindly, just based on the most nodes I can use to

Re: [gmx-users] How can I best setup the nodes number

I think the PME mesh part is ok and it should be less than 0.5 always. Regarding the nodes ask your administrator how many ppn one node have. example suppose if one node has 6 ppn then 12 nodes will have 72ppn which is sufficient to run md. hope the above explanation helps you. Regards Vinoth

RE: [gmx-users] How can I best setup the nodes number

-users-boun...@gromacs.org] on behalf of vinothkumar mohanakrishnan [kmvin...@gmail.com] Sent: Wednesday, October 06, 2010 4:48 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How can I best setup the nodes number I think the PME mesh part is ok and it should be less than 0.5

Re: [gmx-users] How can I best setup the nodes number

- Original Message - From: #ZHAO LINA# zhao0...@e.ntu.edu.sg Date: Wednesday, October 6, 2010 19:44 Subject: [gmx-users] How can I best setup the nodes number To: gmx-users@gromacs.org gmx-users@gromacs.org P {margin-top:0;margin-bottom:0

Re: [gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes

rasoul nasiri wrote: Dear All, Hello I understand one can adjust distance of between solvent molecules by genbox command and -vdwd but I don't know, how do it between the solutes? If you want to place several identical solutes with genbox -ci, then you could copy the file vdwradii.dat

[gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes

Dear All, Hello I understand one can adjust distance of between solvent molecules by genbox command and -vdwd but I don't know, how do it between the solutes? Thanks for helping! Rasoul -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes

rasoul nasiri wrote: Dear All, Hello I understand one can adjust distance of between solvent molecules by genbox command and -vdwd but I don't know, how do it between the solutes? Position your solutes using editconf -center, then add solvent. -Justin Thanks for helping! Rasoul

Re: [gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes

Dear Justin, Hello again Thanks for the message. I want to increase the distance between solutes in simulation box before MD simulation. How can I do it? Rasoul On Sat, Apr 17, 2010 at 5:16 PM, Justin A. Lemkul jalem...@vt.edu wrote: rasoul nasiri wrote: Dear All, Hello I understand

Re: [gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes

rasoul nasiri wrote: Dear Justin, Hello again Thanks for the message. I want to increase the distance between solutes in simulation box before MD simulation. How can I do it? You can't. If you know you need a certain distance, that should be part of your planning :) I suppose you

Re: [gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes

Justin A. Lemkul wrote: rasoul nasiri wrote: Dear Justin, Hello again Thanks for the message. I want to increase the distance between solutes in simulation box before MD simulation. How can I do it? You can't. If you know you need a certain distance, that should be part of your

Re: [gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes

Hi, Thanks for the replies. Since I want to increase distance among co-solvents with themselves and with solutes, i must firstly fill the co-solvents along solutes and solvents after that i remove solvent, finally by edittconf -translate the co-solvents uniformally is distributed in the

Re: [gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes

rasoul nasiri wrote: Hi, Thanks for the replies. Since I want to increase distance among co-solvents with themselves and with solutes, i must firstly fill the co-solvents along solutes and solvents after that i remove solvent, finally by edittconf -translate the co-solvents uniformally is

Re: [gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes

Thanks for the information. Because of haven't satisfactory model from my co-solvent and I have to add it randomly along with the solvent by genbox -ci -nmol. the reason of this criteria relate to crash of system (solute+co-solvent+solvent) in the first step of simulation, because small distance

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

Dear Justin, Thank you for your message. I have found some experimental evidence to suggest that the secondary structure information of protein how change during the reaction of the unfolding. In the other hand, I have percentage of the secondary structure information (%alpha-Helix, %beta-sheet

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

rasoul nasiri wrote: Dear Justin, Thank you for your message. I have found some experimental evidence to suggest that the secondary structure information of protein how change during the reaction of the unfolding. In the other hand, I have percentage of the secondary structure information

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

Hi, Thank you for your quick reply. Is there another CGFF for this purpose that Gromacs can read it? What is your opinion about CG GO model? Kind regards Rasoul On Mon, Dec 21, 2009 at 8:23 PM, Justin A. Lemkul jalem...@vt.edu wrote: rasoul nasiri wrote: Dear Justin, Thank you for your

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

rasoul nasiri wrote: Hi, Thank you for your quick reply. Is there another CGFF for this purpose that Gromacs can read it? What is your opinion about CG GO model? There are several CG models out there, but I don't know much about them. The nice thing about Gromacs is that it can use any

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

For a detailed description of how to set up protein simulation, I recomend you to read the Martini Tutorial on http://md.chem.rug.nl/~marrink/MARTINI/Tutorial.html there you will find step by step instructions along with some explanations of what you are actually doing. In this case you only want

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

Dear Cesar, Thank you for your reply, There are two different kind of water gro in this site (one of them is water.gro in : http://md.chem.rug.nl/~marrink/MARTINI/Coordinates.html and another is water-1bar-303k.gro in : http://md.chem.rug.nl/~marrink/MARTINI/Tutorial.html . Is there difference

[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

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

[gmx-users] how can i coarse grained the protein atomic structure

Dear User, i simulated the lysozyme protein in atomic level and now i'm going to coarse grained it. i'm working with Martini's filester. but i don't know how can i coarse grained my atomic.pdb file to cg.pdb? is there anyone who could help me? Regards, -- gmx-users mailing list

Re: [gmx-users] how can i coarse grained the protein atomic structure

nafiseh farhadian wrote: Dear User, i simulated the lysozyme protein in atomic level and now i'm going to coarse grained it. i'm working with Martini's filester. but i don't know how can i coarse grained my atomic.pdb file to cg.pdb? is there anyone who could help me? Please refer to

[gmx-users] How can i make the DSSP picture like picture 8.10 in the Maunual ?

Hi I have installed DSSP and GIMP. Also I have done some cases with DSSP and GIMP. With GIMP, I did not get the coordinates written as residues vs time(ps). I also did not get the bottom bar in the picture 8.10 in the Manual. Coil Bend Turn A-Helix B-Bridge How can I make the DSSP picture like

Re: [gmx-users] How can i make the DSSP picture like picture 8.10 in the Maunual ?

Chih-Ying Lin wrote: Hi I have installed DSSP and GIMP. Also I have done some cases with DSSP and GIMP. With GIMP, I did not get the coordinates written as residues vs time(ps). I also did not get the bottom bar in the picture 8.10 in the Manual. Coil Bend Turn A-Helix B-Bridge The

[gmx-users] How can I create the OPLS-AA topology file for the liagnd

Hi, i would like to do a ligand -receptor simulation using OPLS-AA force field. I suppose using the options in Gromacs I can create the itp files for protein only. But how can i create the OPLS --AA topology file for the ligand. I think PRODRG server only creates gromacs force field. Please

Re: [gmx-users] How can I create the OPLS-AA topology file for the liagnd

Ms. Aswathy S wrote: Hi, i would like to do a ligand -receptor simulation using OPLS-AA force field. I suppose using the options in Gromacs I can create the itp files for protein only. But how can i create the OPLS --AA topology file for the ligand. I think PRODRG server only creates

Re: [gmx-users] How can I create the OPLS-AA topology file for the liagnd

Mark Abraham wrote: Ms. Aswathy S wrote: Hi, i would like to do a ligand -receptor simulation using OPLS-AA force field. I suppose using the options in Gromacs I can create the itp files for protein only. But how can i create the OPLS --AA topology file for the ligand. I think PRODRG

Re: [gmx-users] How can i know if the protein swell during the MD simulation?

sovent accesible surface area? On Mon, May 18, 2009 at 11:09 AM, Tsjerk Wassenaar tsje...@gmail.comwrote: stretching != swelling, e.g. On Mon, May 18, 2009 at 10:46 AM, Bhanu bhanui...@gmail.com wrote: How about checking radius of gyration??? 2009/5/18 Tsjerk Wassenaar tsje...@gmail.com

Re: [gmx-users] How can i know if the protein swell during the MD simulation?

Well, why didn't I think of that? Maybe because flattening will also increase the SAS, or (partial) unfolding, or opening of two domains... :) Tsjerk On Tue, May 19, 2009 at 6:10 PM, Marius Retegan marius.s.rete...@gmail.com wrote: sovent accesible surface area? On Mon, May 18, 2009 at 11:09

Re: [gmx-users] How can i know if the protein swell during the MD simulation?

Hi, Well, I think 'swelling' is unambiguously, though roughly, defined as 'growing larger', which suggests that you'd have to look for an increase in volume. But how to do that, how to define the volume of the protein is still a matter of setting your criteria and finding the right tools to

Re: [gmx-users] How can i know if the protein swell during the MD simulation?

How about checking radius of gyration??? 2009/5/18 Tsjerk Wassenaar tsje...@gmail.com Hi, Well, I think 'swelling' is unambiguously, though roughly, defined as 'growing larger', which suggests that you'd have to look for an increase in volume. But how to do that, how to define the volume of

Re: [gmx-users] How can i know if the protein swell during the MD simulation?

stretching != swelling, e.g. On Mon, May 18, 2009 at 10:46 AM, Bhanu bhanui...@gmail.com wrote: How about checking radius of gyration??? 2009/5/18 Tsjerk Wassenaar tsje...@gmail.com Hi, Well, I think 'swelling' is unambiguously, though roughly, defined as 'growing larger', which suggests

[gmx-users] How can i know if the protein swell during the MD simulation?

HI How can i know if the protein swell during the MD simulation? What are those indications to see the swollen protein? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search

Re: [gmx-users] How can i know if the protein swell during the MD simulation?

Chih-Ying Lin wrote: HI How can i know if the protein swell during the MD simulation? What are those indications to see the swollen protein? How do you define the term swelling? This again sounds like another issue on defining your own criteria for the expected behavior and reading the

[gmx-users] how can i know the center of the cleft of protein?

Hi how can i know the center of the cleft of protein? I mean how to calculate or use Gromacs to know the center (x,y,z) of the cleft of protein? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] how can i know the center of the cleft of protein?

Chih-Ying Lin wrote: Hi how can i know the center of the cleft of protein? I mean how to calculate or use Gromacs to know the center (x,y,z) of the cleft of protein? This is an ill-defined problem. You could try g_traj with a suitable index file with the surrounding residues. Thank you Lin

[gmx-users] How can I record only molecule trajectory ?

Hi The command mdrun -o traj.trr -x traj.xtc and then, the two files, traj.trr or traj.xtc will record the trajectory of all the molecules of the simulated system. How can I record only molecule trajectory with some command? Thank you Lin ___

Re: [gmx-users] How can I record only molecule trajectory ?

Chih-Ying Lin wrote: Hi The command mdrun -o traj.trr -x traj.xtc and then, the two files, traj.trr or traj.xtc will record the trajectory of all the molecules of the simulated system. How can I record only molecule trajectory with some command? If you mean protein only then check

Re: [gmx-users] How can I record only molecule trajectory ?

Chih-Ying Lin wrote: Hi The command mdrun -o traj.trr -x traj.xtc and then, the two files, traj.trr or traj.xtc will record the trajectory of all the molecules of the simulated system. How can I record only molecule trajectory with some command? Use xtc_grps in the .mdp file, or use

[gmx-users] How can I generate a Input *.gro file of coarse grain model?

Dear all gromacs users: I am trying to use the MARTINI CG force field from Marrink et al. in my simulation. But I don't konw how to generate the input *.gro files. When I use all-atom model, in gromacs I can use genbox editconf et al to generate the input *.gro files. For example, I can use

Re: [gmx-users] How can I generate a Input *.gro file of coarse grain model?

Hi Xuji, You'll have to have a coordinate file to start with, just like with your atomistic scale stuff. Whether this would be .pdb or .gro doesn't matter. If you have don't have coordinates, parameters are pretty useless. Maybe the Groningen guys are willingg to share you a .pdb file to play

Re: [gmx-users] How can I generate a Input *.gro file of coarse grain model?

There are scripts provided on the MARTINI site to generate the necessary structure files, and the topology, IIRC. -Justin xuji wrote: Dear all gromacs users: I am trying to use the MARTINI CG force field from Marrink et al. in my simulation. But I don't konw how to generate the input *.gro

RE: [gmx-users] How can I generate a Input *.gro file of coarse grain model?

. Yang From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of xuji [EMAIL PROTECTED] Sent: Sunday, October 19, 2008 1:47 AM To: gmx-users@gromacs.org Subject: [gmx-users] How can I generate a Input *.gro file of coarse grain model? Dear all gromacs

Re: [gmx-users] How can I generate a Input *.gro file of coarse grain model?

Hi xuji, I do not believe the scripts provided on the site deal with water. That is, unfortunately, you cannot take and equilibrated atomistic system and convert directly to the CG representation. What you will have to do is go to the test/model system page and download the pure water

[gmx-users] How can I install Gromacs on Window XP?

Hello, How can I install Gromacs on Window XP? Thanks a lot! Hero __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing list

Re: [gmx-users] How can I install Gromacs on Window XP?

Hero wrote: Hello, How can I install Gromacs on Window XP? See http://wiki.gromacs.org/index.php/Installation and links thereon. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search

[gmx-users] how can I restart simulation

Dear Gromacs Users, I have done MD simulation for 15 ns and I need simulation for further 5 ns. I am wondering how is this possible? Thank you in advance Anamika ___ gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] how can I restart simulation

Quoting Anamika Awasthi [EMAIL PROTECTED]: Dear Gromacs Users, I have done MD simulation for 15 ns and I need simulation for further 5 ns. I am wondering how is this possible? http://wiki.gromacs.org/index.php/Doing_Restarts This question is often asked; check the archive before

Re: [gmx-users] How can I add ffG43a1p force field to gromacs software?

Hi Try the -ff option of pdb2gmx, if you're not able to get it working. This less complicated. pdb2gmx -f pdb.pdb -ff ffG43a1 Should work Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077

Re: [gmx-users] How can I add ffG43a1p force field to gromacs software?

Dear Goette Thanks a lot for your helpful suggestion. Cheers Maik Goette [EMAIL PROTECTED] wrote: Hi Try the -ff option of pdb2gmx, if you're not able to get it working. This less complicated. pdb2gmx -f pdb.pdb -ff ffG43a1 Should work Regards Maik Goette, Dipl. Biol. Max Planck

Re: [gmx-users] How can I add ffG43a1p force field to gromacs software?

Mitra Kheirabadi wrote: Dear Goette Thanks a lot for your helpful suggestion. Please do feel free to thank people for their contribution, however I'd suggest doing it off the list. There are hundreds of people subscribed, and most of them don't need to read your reply of thanks to most of

Re: [gmx-users] How can I add ffG43a1p force field to gromacs software?

Dear Mark Thank you very much for your helpful suggestions. sincerly Mark Abraham [EMAIL PROTECTED] wrote: Mitra Kheirabadi wrote: Dear Dr.Periole I add ffG43a1p to FF.dat/ top and changed 11 to 12 on this file but sorry again I did not appear. please help me. The new

Re: [gmx-users] How can I add ffG43a1p force field to gromacs software?

Hi Mitra, You can add it in the file FF.dat in the $GMXDIR/share/gromacs/top/ directory. Cheers, Tsjerk On Jan 8, 2008 3:35 PM, Mitra Kheirabadi [EMAIL PROTECTED] wrote: Dear Dr. Smith I want to run a virus phosphorylated protein by gromacs. Furtunatly, you construct related force field

[gmx-users] How can I add ffG43a1p force field to gromacs software?

Dear Dr. Smith I want to run a virus phosphorylated protein by gromacs. Furtunatly, you construct related force field by ffG43A1p name. I copied this force field to top. file gromacs but when I constructed pdbgmx, there is no any ffG43a1p to select. Could you help me? I be so grateful

Re: [gmx-users] How can I add ffG43a1p force field to gromacs software?

On Tue, 8 Jan 2008 06:35:28 -0800 (PST) Mitra Kheirabadi [EMAIL PROTECTED] wrote: Dear Dr. Smith I want to run a virus phosphorylated protein by gromacs. Furtunatly, you construct related force field by ffG43A1p name. I copied this force field to top. file gromacs but when I constructed

Re: [gmx-users] How can I add ffG43a1p force field to gromacs software?

Dear Periola I appreciate your kindly help. Respectfully Xavier Periole [EMAIL PROTECTED] wrote: On Tue, 8 Jan 2008 06:35:28 -0800 (PST) Mitra Kheirabadi wrote: Dear Dr. Smith I want to run a virus phosphorylated protein by gromacs. Furtunatly, you construct related force field

Re: [gmx-users] How can I add ffG43a1p force field to gromacs software?

Dear Dr.Periole I add ffG43a1p to FF.dat/ top and changed 11 to 12 on this file but sorry again I did not appear. please help me. Respectfully Mitra Kheirabadi [EMAIL PROTECTED] wrote: Dear Periola I appreciate your kindly help. Respectfully Xavier Periole [EMAIL

Re: [gmx-users] How can I add ffG43a1p force field to gromacs software?

Mitra Kheirabadi wrote: Dear Dr.Periole I add ffG43a1p to FF.dat/ top and changed 11 to 12 on this file but sorry again I did not appear. please help me. The new forcefield files have to go to the same location as the old ones, in the subdirectory something like share/gromacs/top. Or

[gmx-users] How can I add hydrogen?

Dear gmx users I run a simulation of the liquid of acetonitrila (OPLS-UA) and I need of the configurations with explicit hydrogen atoms. Somebody could help me add the H atoms to configurations? eef -- ___ Eudes Eterno Fileti Centro de Ciência Naturais e

Re: [gmx-users] How can I make commands non-interactive?

23 apr 2007 kl. 21.31 skrev David van der Spoel: Arthur Roberts wrote: Hi, all, I need to be able to execute commands by a script and I need the commands to be non-interactive. One example of the commands that I use is g_rms. echo 3 3 | g_rms flags Or (inside a script) g_rms -flags EOF

[gmx-users] How can I make commands non-interactive?

Hi, all, I need to be able to execute commands by a script and I need the commands to be non-interactive. One example of the commands that I use is g_rms. How can I make this command totally non-interactive? Thank you in advance, Best wishes, Art Roberts University of Washington Department

Re: [gmx-users] How can I make commands non-interactive?

Arthur Roberts wrote: Hi, all, I need to be able to execute commands by a script and I need the commands to be non-interactive. One example of the commands that I use is g_rms. echo 3 3 | g_rms flags How can I make this command totally non-interactive? Thank you in advance, Best

[gmx-users] How can I uninstall the old version?

Dear gmx users: I am a novice. I want to install a new version Gromacs, but there is an old version in my computer. How can I uninstall the old version? Thank you! ___ gmx-users mailing listgmx-users@gromacs.org

Re:[gmx-users] How can I uninstall the old version?

. In your mail: From: Àîî£ [EMAIL PROTECTED] Reply-To: Àîî£ [EMAIL PROTECTED], Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] How can I uninstall the old version? Date:Sun, 04 Feb 2007 21:33:51 +0800 Dear gmx users: I am a novice. I want to install

[gmx-users] How can I generate a FCC unit cell?

Hi gmx-users, I need to generate a FCC unit cell (in fact a face centered cubic lattice) in order to produce a nanocristal. I would like to know if is possible to make this using directly GROMACS. In affirmative case, as I can make it? Thanks in advance ___

Re: [gmx-users] How can I generate a FCC unit cell?

Eudes Fileti wrote: Hi gmx-users, I need to generate a FCC unit cell (in fact a face centered cubic lattice) in order to produce a nanocristal. I would like to know if is possible to make this using directly GROMACS. In affirmative case, as I can make it? Thanks in advance

RE: [gmx-users] How can I remove water and ion molecules

Or you could try using the make_ndx utility, make an index file with one of the groups containing all the molecules you want to keep, then run either editconf (if want to remove them from the .gro / .pdb files) or trajconv (if want to remove them from trajectory files). Catch ya, Dr. Dallas

[gmx-users] How can I remove water and ion molecules

Hi,How can I remove water and ion molecules from the pdb file after energy minimization and molecular dynamic simulation?Thank you very much.Sincerely yours,Jahanshah Ashkani,PhD student of Biotechnology Genetics,University of the Western Cape,Biotechnology Department,Private Bag X17,7735

Re: [gmx-users] How can I remove water and ion molecules

jahanshah ashkani wrote: Hi, How can I remove water and ion molecules from the pdb file after energy minimization and molecular dynamic simulation? From a pdb file is easy - just get a text editor and delete those lines. Never mind about the atom or residue numbering. Is this the question

Re: [gmx-users] How can I remove water and ion molecules

(the particular lipid you are using) cheers Kia Message: 8 Date: Tue, 26 Sep 2006 01:37:43 +1000 From: Mark Abraham [EMAIL PROTECTED] Subject: Re: [gmx-users] How can I remove water and ion molecules To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED

Re: [gmx-users] How can I remove water and ion molecules

man grep with special attention to -v option bounus ball: it also works before em and md Cheers On Monday 25 September 2006 15:55, jahanshah ashkani wrote: Hi, How can I remove water and ion molecules from the pdb file after energy minimization and molecular dynamic simulation? Thank you

Re: [gmx-users] How can I remove water and ion molecules

make an index file entry with the stuff you want to write in your pdb, and use editconf -n to dump only that. On Sep 25, 2006, at 5:05 PM, Guillem Portella wrote: man grep with special attention to -v option bounus ball: it also works before em and md Cheers On Monday 25 September