[gmx-users] trajectory file in the VMD

Hi all users, When I try to input the .gro and .trr file into the VMD, I always find that there is no bond connected among the atoms.But in fact, I have defined all the bond connection in the gromacs files. Can anyone tell me how to get the snap shots in the VMD with the bonds among the atoms?

[gmx-users] input the gro and trr file into the VMD

Hi all users, When I try to input the .gro and .trr file into the VMD, I always find that there is no bond connected among the atoms.But in fact, I have defined all the bond connection in the gromacs files. Can anyone tell me how to get the snap shots in the VMD with the bonds among the atoms?

Re: [gmx-users] Re: grompp error- Excluding 3 bonded neighbours-Fatal (Dean Cuebas)

Dean Cuebas wrote: Dean Cuebas wrote: Dear users, I¹ve been trying to reproduce the GROMACS tutorial for Drug _ Enzyme Complex I¹ve tried to get grompp to work, but I keep getting the following message: ___ creating statusfile for 1 node... B

[gmx-users] Re: grompp error- Excluding 3 bonded neighbours-Fatal (Dean Cuebas)

>> >> Dean Cuebas wrote: >> Dear users, >> I¹ve been trying to reproduce the GROMACS tutorial for Drug _ Enzyme Complex >> >> I¹ve tried to get grompp to work, but I keep getting the following message: >> ___ >> >> creating statusfile for 1 nod

Re: [gmx-users] Problem in preparation of the enzyme/substrate complex

Ji Liu wrote: Hello everyone, I'm gonna run MD simulation with a enzyme/substrate system. Here the substrate must connected with the side chain of an activity residue of enzyme through covalent bond. However, i really have no idea about the preparation of such a complex structure file. Actual

[gmx-users] Problem in preparation of the enzyme/substrate complex

Hello everyone, I'm gonna run MD simulation with a enzyme/substrate system. Here the substrate must connected with the side chain of an activity residue of enzyme through covalent bond. However, i really have no idea about the preparation of such a complex structure file. Actually, i tried to modi

Re: [gmx-users] problem in gromacs installation

nitu sharma wrote: *Dear All, I have compiled fft-3.2.1 in a specific user directory; then configured, compiled gromacs-4.0.3 from source code according to directions and installed it in the specific directory, all without any errors, but at the end "make tests" command fails, the output is:

[gmx-users] problem in gromacs installation

*Dear All, I have compiled fft-3.2.1 in a specific user directory; then configured, compiled gromacs-4.0.3 from source code according to directions and installed it in the specific directory, all without any errors, but at the end "make tests" command fails, the output is: (if test -d "gmxtest";

RE: [gmx-users] gromacs-4.0.2, parallel performance in two quad core xeon machines

Hi, Oops, I meant 72000, which is only a factor of 10. I guess it might be faster one two nodes then, but probably not 2 times. If you use PME you can also experiment with putting all the PME nodes on one machine and the non-PME nodes on the other, probably with mdrun -ddorder pp_pme Gromacs sup

RE: [gmx-users] gromacs-4.0.2, parallel performance in two quad core xeon machines

Hello,thank you for your answer. I just wondering though. How am I supposed to have a system with more than 9 atoms, while the gro file has a fixed format giving up to 5 digits in the number of atoms?  What else should I change in order to succeed better performance from my hardware if I can

[gmx-users] Gromac 4 support in Chimera

Hi all, For those of you using Chimera to work with your Gromacs trajectories, I just added support for Gromacs 4 .tpr files to Chimera. This capability is only available in daily builds right now. You can get a daily build by going to the UCSF Chimera Home Page and following the "Daily

RE: [gmx-users] combination rules -- the part about the combination rules

Hi, No pairtypes are for bonded pair interactions, not for combinations of non-bonded interactions. The manual tells you how to do this: [ nonbond_params ] A_ii A_jj 2 a b c6 Berk > Date: Wed, 18 Feb 2009 13:31:43 -0500 > From: chris.ne...@utoronto.ca > To: gmx-users@gromacs.org > Subject:

RE: [gmx-users] anomalous free energy dgdl.xvg values every nstlist steps while using a twin-range cutoff

Hi, This was a new issue in 4.0, 3.3 was fine. Berk > Date: Wed, 18 Feb 2009 13:26:39 -0500 > From: chris.ne...@utoronto.ca > To: gmx-users@gromacs.org > Subject: [gmx-users] anomalous free energy dgdl.xvg values every nstlist > steps while using a twin-range cutoff > > Thanks Berk, 4.0.

[gmx-users] combination rules -- the part about the combination rules

For LJ interactions, use [ pairtypes ]. For Coulombics there is unfortunately no analogous solution. I am not clear about exactly what you want to do. What "parameters" are you interested in, or by this do you just mean LJ and Q? Chris. -- original message -- Hello, I was wondering ho

[gmx-users] anomalous free energy dgdl.xvg values every nstlist steps while using a twin-range cutoff

Thanks Berk, 4.0.4 does show the expected behaviour for me with the twin-range cutoff. Since I obtained 4.0.4 prior to mentioning this issue, I gather that you gave the free energy code a good looking-over recently. I really appreciate it. I have seen only one previous paper that utilized a

Re: [gmx-users] combination rules

Shuangxing Dai wrote: I also have problem in installing xmgr. I use MacOSX 10.5.5. I type ./configure and got this error messege: ecme222-96-dhcp:xmgr-4.1.2 ssx$ ./configure creating cache ./config.cache checking host system type... configure: error: can not guess host type; you must speci

[gmx-users] combination rules

Hello, I was wondering how to set up parameters for interactions between two different atoms A and B. Since for Gromacs parameters are defined to each kind of atom, I cannot specify parameters between A and B. For Buckingham potential, the rule was: A_ij=(A_ii * A_jj)^(1/2) So anyone know

[gmx-users] gromacs-4.0.2, parallel performance in two quad core xeon machines

Hello, we have built a cluster with nodes that are comprised by the following: dual core Intel(R) Xeon(R) CPU E3110 @ 3.00GHz. The memory of each node has 16Gb of memory. The switch that we use is a dell power connect model. Each node has a Gigabyte ethernet card. I tested the performance for

[gmx-users] g_spatial and vmd volume slice

Dear XAvier, "I have played with this recently and could not find the way to set or change the colors on the volume slice." see my previous post about how to do this with black/white and gimp/ photoshop I did not find any mention of this in your previous post. But it is ok. Sorry for

[gmx-users] g_mdmat

Hello list, does g_mdmat ouput the standard deviation that goes along with the mean.xpm file? Thank you. -Rob _ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org

RE: [gmx-users] ewald_rtol parameter question

> Date: Thu, 19 Feb 2009 01:53:47 +1100 > From: mark.abra...@anu.edu.au > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] ewald_rtol parameter question > > Claus Valka wrote: > > Hello, > > > > I would like to ask you a (simple) clarification question: > > Reading the manual and equations

Re: [gmx-users] Genbox problem with TIP4P water with OPLS

On Thu, Feb 19, 2009 at 01:56:28AM +1100, Mark Abraham wrote: > Chao Zhang wrote: > >Hi Mark, > > > >I think 3.3.2, does it be fixed in 4.0? > > I don't know - I've not seen it reported. You should search the mailing > list archives. I've solvated with tip4p in 3.3cvs and 3.3.1, never had the pr

Re: [gmx-users] Genbox problem with TIP4P water with OPLS

Chao Zhang wrote: Hi Mark, I think 3.3.2, does it be fixed in 4.0? I don't know - I've not seen it reported. You should search the mailing list archives. There won't be any interest in diagnosing or fixing it within version 3.x, but if you can reproduce your result in 4.0.4, file a bugzill

Re: [gmx-users] ewald_rtol parameter question

Claus Valka wrote: Hello, I would like to ask you a (simple) clarification question: Reading the manual and equations 4.158 up to 4.160 there is a convergence parameter b (with hellenic letters β). I would like to ask you whether this parameter is the same as the ewald_rtol that I come accross

Subject: [gmx-users] gromacs QM/MM

Although there is not much interface specific information, you can check one of our recent papers, eg. L.V. Schaefer et al., PLoS computational biology, 4 (2008), e134. More information on how to build up the interface on the gaussian side you find on wwwuser.gwdg.de/~ggroenh Gerrit -

[gmx-users] ewald_rtol parameter question

Hello, I would like to ask you a (simple) clarification question: Reading the manual and equations 4.158 up to 4.160 there is a convergence parameter b (with hellenic letters β). I would like to ask you whether this parameter is the same as the ewald_rtol that I come accross in the manual. If it

[gmx-users] ewald_rtol parameter question

Hello,I would like to ask you a (simple) clarification question:Reading the manual and equations 4.158 up to 4.160 there is a convergence parameter b (with hellenic letters β).I would like to ask you whether this parameter is the same as the ewald_rtol that I come accross in the manual. If it is

Re: [gmx-users] g_spatial and vmd volume slice

"I have played with this recently and could not find the way to set or change the colors on the volume slice." see my previous post about how to do this with black/white and gimp/ photoshop I did not find any mention of this in your previous post. But it is ok. "Moreover I found that the

Re: [gmx-users] R: R: help with neighborsearching error

Anna Marabotti wrote: Dear Justin, just to answer to your comments: certainly I'm not expecting that things are going EXACTLY in the same way every time I repeat them, but it seems quite strange to me that the first time the system arrives to convergence and the next time not, with the same p

Re: [gmx-users] Genbox problem with TIP4P water with OPLS

Hi Mark, I think 3.3.2, does it be fixed in 4.0? Chao On Wed, Feb 18, 2009 at 12:06 PM, Mark Abraham wrote: > Chao Zhang wrote: > >> Dear gmx-user, >> >> I try to build a pure water box in Gromacs, so I just solved one water as >> solute with genbox. >> >> When I use tip3p water, my scripts wor

[gmx-users] gromacs QM/MM

Hi I would like to use the gromacs/Gaussian03 interface and i would like to know if there are any papers with data obtained using this interface. Thanks a lot Jacopo ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/lis

Re: [gmx-users] Genbox problem with TIP4P water with OPLS

Chao Zhang wrote: Dear gmx-user, I try to build a pure water box in Gromacs, so I just solved one water as solute with genbox. When I use tip3p water, my scripts work well. But to switch to tip4p water, there seems a bug, I don't know whether people have noticed this or not. The system sh

[gmx-users] R: R: help with neighborsearching error

Dear Justin, just to answer to your comments: certainly I'm not expecting that things are going EXACTLY in the same way every time I repeat them, but it seems quite strange to me that the first time the system arrives to convergence and the next time not, with the same parameters... The other thi

[gmx-users] Genbox problem with TIP4P water with OPLS

Dear gmx-user, I try to build a pure water box in Gromacs, so I just solved one water as solute with genbox. When I use tip3p water, my scripts work well. But to switch to tip4p water, there seems a bug, I don't know whether people have noticed this or not. The system shows that it added 350 wat

[gmx-users] Re: grompp error- Excluding 3 bonded neighbours-Fatal error

> dear dean, there is no problem with your mdp file. for grompp number of atoms in .top file and input .gro file should be equal,look your.top file, this may be because u have added number of ions in your .top file but it not present in your .gro file( difference of 8 atom only in both file, which

Re: [gmx-users] grompp error- Excluding 3 bonded neighbours-Fatal error

Dean Cuebas wrote: Dear users, I¹ve been trying to reproduce the GROMACS tutorial for Drug _ Enzyme Complex I¹ve tried to get grompp to work, but I keep getting the following message: ___ creating statusfile for 1 node... Back Off! I just ba

[gmx-users] RE: NVT or NPT ?

>I read some papers and it seems that more simulation system is under NPT. > >What is the benefit for running MD under NPT? Not every model gives a correct (experimental) density using NPT. -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry National University of Kharkiv Svoboda sq., 4, Khark

Re: [gmx-users] NVT or NPT ?

And not to forget: most experiments are performed under (more or less) constant pressure. In that sense, NPT simulations are 'more like the real thing'. Cheers, Tsjerk On Wed, Feb 18, 2009 at 5:21 AM, wrote: > short answer: volume equilibration and therefore density equilibration. Even > peopl

[gmx-users] grompp error- Excluding 3 bonded neighbours-Fatal error

Dear users, I¹ve been trying to reproduce the GROMACS tutorial for Drug _ Enzyme Complex I¹ve tried to get grompp to work, but I keep getting the following message: ___ >> creating statusfile for 1 node... >> >> Back Off! I just backed up mdout