Re: [gmx-users] Adding ions

2009-11-19 Thread Amir Marcovitz
Hi, Make sure you do specify the explicit names of the topology and structure file. in the mannual they omit the suffix of the file. for the purpose of rigourism - this is the line i'm using: genion -pname Na+ -nname Cl- -o file_ionized.gro -conc 0.2 -p topol.top On Tue, Nov 17, 2009

[gmx-users] covariance

2009-11-19 Thread Morteza Khabiri
Dear gmxuser I want to compare a dimer covariance which was already run in 2 different situation. The problem is that the scale of produced covariance (which produced by -xpma) in 2 case is different e.g the scale for one of them start from -0.18 to 0.05 and other -0.15 to 0.052. Is there any poss

RE: SV: SV: SV: [gmx-users] Hydrogen bonding

2009-11-19 Thread Sarah Witzke
-Original Message- From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul Sent: Thu 19-11-2009 02:09 To: Gromacs Users' List Subject: Re: SV: SV: SV: [gmx-users] Hydrogen bonding Sarah Witzke wrote: > > > Sarah Witzke wrote: > > > >> ARRGH, I'm sorry, things went too

[gmx-users] How to make carbon nanotube infinite?

2009-11-19 Thread Cun Zhang
Hi,gmx users, I want to set CNT infinite in the system of CNT and water.  I'm using GMX 4.1,so I have set pbc=xyz, periodic_molecules=yes in mdp file. I set the box size larger than CNT's length a C-C bond(half up and half down).  If I don't do a EM, it will crumble. But if I do it,it can't satisfy

Re: SV: SV: SV: [gmx-users] Hydrogen bonding

2009-11-19 Thread Justin A. Lemkul
Sarah Witzke wrote: -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul Sent: Thu 19-11-2009 02:09 To: Gromacs Users' List Subject: Re: SV: SV: SV: [gmx-users] Hydrogen bonding Sarah Witzke wrote: Sarah Witzke wrote: ARRGH, I'm sorry, things w

Re: [gmx-users] How to make carbon nanotube infinite?

2009-11-19 Thread Justin A. Lemkul
Cun Zhang wrote: Hi,gmx users, I want to set CNT infinite in the system of CNT and water. I'm using GMX 4.1,so I have set pbc=xyz, periodic_molecules=yes in mdp file. Not possible, Gromacs 4.1 hasn't been released :) If you're using version 4.0.1, you shouldn't, because it has a nasty bug

Re: [gmx-users] covariance

2009-11-19 Thread Tsjerk Wassenaar
Hi Morteza, Your question suggests a lack of understanding of the principles (not principals) of covariance analysis. It is probably best to read a bit more on the background of this technique, until you realize what it is, what it can do, and what it can't. There are a number of discussions archi

[gmx-users] Force Fields

2009-11-19 Thread Smith, Chanel Chonda
What are the main differences between the force fields used in gromacs? In which scenarios are each force field better to use? Chanel -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search

Re: [gmx-users] Force Fields

2009-11-19 Thread Justin A. Lemkul
Smith, Chanel Chonda wrote: What are the main differences between the force fields used in gromacs? In which scenarios are each force field better to use? I think this question is best addressed by a thorough examination of the literature and the various textbooks that exist regarding sim

[gmx-users] covariance

2009-11-19 Thread Morteza Khabiri
Dear Tsjerk Thanks for your help and reply. I thing my question was not clear. I want to compare 2 covariance map. but in one map the red colour shows e.g 1 nm^2 fluctuation and in other map the red colour shows e.g 0.5 nm^2 fluctuation. I wanted that both map be in the same scale of colour inten

[gmx-users] Hydrated radius of ions

2009-11-19 Thread Manik Mayur
Hi, Is there any gromacs utility to calculate the hydrated radius of ions? Thanks, Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search th

[gmx-users] H-bonds in water + alcohol mixture

2009-11-19 Thread Nuno Garrido
Dear all, I'm trying to evaluate the number of H-bonds in a 150 alcohol (TraPPE) + 57 water (SPC/E) molecules mixture. >From rdf analysis I can observe that the most prominent peak is related to OW-OW group, followed by OW-OH group and finally OH-OH group. OW = water oxygen OH = alcohol oxygen.

Re: [gmx-users] How to make carbon nanotube infinite?

2009-11-19 Thread Cun Zhang
Justin, thanks for your reply. By the way, your GMX tutorials is great! I post the gro file and mdp file at the end. On Thu, Nov 19, 2009 at 10:09 PM, Justin A. Lemkul wrote: > > Not possible, Gromacs 4.1 hasn't been released :) If you're using version > 4.0.1, you shouldn't, because it has a

[gmx-users] FEP with bond formation, pair problem

2009-11-19 Thread Jochen Hub
Hi, how can I use different coulomb 1-4 interactions in the A and B state. The Manual just says [ pairs ] : LJ and Coulomb 1-4 interactions but, I far as I could see, did not give an example how the coulomb 1-4 interaction can be explicitly given. Thanks a lot for any help, Jochen -- --

Re: [gmx-users] How to make carbon nanotube infinite?

2009-11-19 Thread Justin A. Lemkul
Cun Zhang wrote: I mean, I make the distance of the top ( or bottom ) C atoms in CNT and the corresponding edge of the box equals the length of a C-C bond( about 0.142nm ). OK, that sounds reasonable, but did you define the periodic bonds appropriately? Your original question was that

Re: [gmx-users] covariance

2009-11-19 Thread Tsjerk Wassenaar
Hi Morteza, To me, your initial question seemed to relate to scaling/constraining the covariances. But I also take most any opportunity to warn people not to think too ligthly about PCA :) You can use xpm2ps to combine the matrices and recolorize according to the range of the combined set. Hope i

RE: [gmx-users] FEP with bond formation, pair problem

2009-11-19 Thread Berk Hess
Hi, There are automatically different, since they are based on the A and B state charges and the A and B state atom types. Berk > Date: Thu, 19 Nov 2009 16:15:52 +0100 > From: joc...@xray.bmc.uu.se > To: gmx-users@gromacs.org > Subject: [gmx-users] FEP with bond formation, pair problem > > Hi

[gmx-users] Re: Force Fields

2009-11-19 Thread Vitaly V. Chaban
The selection of FF depends on what you study. Perhaps, none of them will be useful for you. The existing ones differ at least by the procedures if generation although many parameters are very close. > > What are the main differences between the force fields used in gromacs?  In > which scenarios

Re: [gmx-users] FEP with bond formation, pair problem

2009-11-19 Thread David van der Spoel
Berk Hess wrote: Hi, There are automatically different, since they are based on the A and B state charges and the A and B state atom types. But the problem is more complicated: Let's say there is a Butane radical C4H9. that you want to bond to another butane radical to form octane (C8H18).

Re: [gmx-users] FEP with bond formation, pair problem

2009-11-19 Thread Jochen Hub
David van der Spoel wrote: Berk Hess wrote: Hi, There are automatically different, since they are based on the A and B state charges and the A and B state atom types. But the problem is more complicated: Let's say there is a Butane radical C4H9. that you want to bond to another butane rad

[gmx-users] 6-31G** for Gromacs

2009-11-19 Thread ilona . baldus
Hi Gerrit, I would like to use 6-31G** for my QMMM-calculation. Since sulfur is part of my QM system, I consider that a sensible thing to do. Unfortunately, it is not implemented in Gromacs, so I tried to add that bit myself. Here's the point where I got stuck: src/mdlib/qm_gaussian.c

Re: [gmx-users] 6-31G** for Gromacs

2009-11-19 Thread Mark Abraham
ilona.bal...@bioquant.uni-heidelberg.de wrote: Hi Gerrit, I would like to use 6-31G** for my QMMM-calculation. Since sulfur is part of my QM system, I consider that a sensible thing to do. Unfortunately, it is not implemented in Gromacs, so I tried to add that bit myself. Here's the point

[gmx-users] Problem with Gromacs-CPMD

2009-11-19 Thread jorge_quintero
Dear all, I'm running some simulations using Gromacs/CPMD but it doesn't continue during QMCONTINUE file lecture. See below: EXTERNAL ENERGY= 5.867019924829098E-002 AU REAL TOTAL ENERGY = -97.3517503273190 AU ATOM COORDINATESGRADIENTS (-FORCES) 1 C

RE: [gmx-users] Hydrated radius of ions

2009-11-19 Thread Dallas B. Warren
g_rdf ? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a ha

[gmx-users] How to check for bad contacts

2009-11-19 Thread Lum Nforbi
Hello, How do you check for bad contacts in a system that cannot be minimized? Thanks, Lum -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subsc

RE: [gmx-users] How to check for bad contacts

2009-11-19 Thread Dallas B. Warren
When you try to minimise, it will typically tell you the worst offending atoms in your system. Which you can then check visually using VMD etc and try and work out why it is an issue. Then you can adjust how the system was set up to fix the issue. Also, if you just look at the system visually

[gmx-users] User results for another run

2009-11-19 Thread Jack Shultz
I must have asked this before but I'm trying find the answer again. If I want to use the results from mdrun for another run following the first time interval, what do I need to do? -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.or

Re: [gmx-users] User results for another run

2009-11-19 Thread Justin A. Lemkul
Jack Shultz wrote: I must have asked this before but I'm trying find the answer again. If I want to use the results from mdrun for another run following the first time interval, what do I need to do? http://www.gromacs.org/Documentation/How-tos/Extending_Simulations -Justin -- =

RE: [gmx-users] User results for another run

2009-11-19 Thread Dallas B. Warren
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167

[gmx-users] g_msd => The MSD and periodic boundary condition

2009-11-19 Thread Chih-Ying Lin
Hi With the periodic boundary condition, all the recorded coordinates of the atom are within the simulation box. To calculate the MSD, the movement of the center mass of the molecules between this time step with the next time step is calculated without considering the periodic boundary condition. B

Re: [gmx-users] g_msd => The MSD and periodic boundary condition

2009-11-19 Thread Justin A. Lemkul
Chih-Ying Lin wrote: Hi With the periodic boundary condition, all the recorded coordinates of the atom are within the simulation box. To calculate the MSD, the movement of the center mass of the molecules between this time step with the next time step is calculated without considering th

[gmx-users] how to make a porcupine plot?

2009-11-19 Thread AntonioLeung
Hi, all, I am newcomer of gmx, and I want to know how to make a porcupine plot after a essential MD. I found it looks nicer than linear interpolations between two extremes. Thanks in advance! Atonio-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-

Re: [gmx-users] how to make a porcupine plot?

2009-11-19 Thread Justin A. Lemkul
AntonioLeung wrote: Hi, all, I am newcomer of gmx, and I want to know how to make a porcupine plot after a essential MD. I found it looks nicer than linear interpolations between two extremes. Thanks in advance! There are not tools in Gromacs to do such a thing, but a simple Google search