[gmx-users] mismatch between energies of sequential minimization runs

Hi, I am running 2 sequential minimizations with the same mdp file. As expected the second minimization stops in step zero and the resulting structures of the 2 minimization runs are identical (RMSD=0.0). But, the energies of the last step of the first minimization (step 14) and the zero step

[gmx-users] RE: simulation of a metal binding sites

Hi, There are methodological difficulties in simulating multivalent ions together with proteins. Check the mailing list for a discussion and reference. This is not an issue of Gromacs but of dealing with protein-ion interactions using a classical non-polarisable force field. Check the

Re: [gmx-users] Re: gromacs QM/MM compilation with gaussian (Txema Mercero)

On Wed, Feb 16, 2011 at 2:44 PM, Gerrit Groenhof ggro...@gwdg.de wrote: What is your path to the gaussian executable? GAUSS_EXE=/software/g03gromacs/g03 GAUSS_DIR=/software/g03gromacs/g03 In this directories are all gaussian l*.exe files. DEVEL_DIR=/software/g03gromacs/g03/modlinks Txema

[gmx-users] R. Re: Re: gromacs QM/MM compilation with gaussian (Txema Mercero) (Txema Mercero)

2. Re: Re: gromacs QM/MM compilation with gaussian (Txema Mercero) (Txema Mercero) Can you send me your tpr file? Gerrit -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] R. Re: Re: gromacs QM/MM compilation with gaussian (Txema Mercero) (Txema Mercero)

Here it goes. On Thu, Feb 17, 2011 at 9:49 AM, Gerrit Groenhof ggro...@gwdg.de wrote:   2. Re: Re: gromacs QM/MM compilation with gaussian (Txema      Mercero) (Txema Mercero) Can you send me your tpr file? Gerrit -- gmx-users mailing list    gmx-users@gromacs.org

Re: [gmx-users] R. Re: Re: gromacs QM/MM compilation with gaussian (Txema Mercero) (Txema Mercero)

Hi, With gmx 5.5.3 your input works here. Still it crashes in g09, but that is because you have a multiplicity of 1 with 181 electrons. QM/MM calculation requested. there we go! Layer 0 nr of QM atoms 24 QMlevel: RHF/6-31G number of CPUs for gaussian = 1 memory for gaussian = 5000

Re: [gmx-users] R. Re: Re: gromacs QM/MM compilation with gaussian (Txema Mercero) (Txema Mercero)

Thanks Gerrit, Do you have any guess whether the problem could in in gromacs or Gaussian compilation? In the lines you sent me in your execution I see Calling '/home/ggroenh/g09//g09 input.com input.log But I do not see something like this in our exectution. By the way are there somewhere

Re: [gmx-users] Protein-membrane system

Jianguo Li wrote: Hi, 3000 water molecule per lipids per second corresponds to 0.000384 water molecules transferred across the membrane per nano second (assume the system contains 128 lipids). It seems water translocation should not be observed in a simulation of 10 ns, but I am not sure.

Re: [gmx-users] initial structures for md simulations

packmol and hyperchem can do it for u. On Wed, Feb 16, 2011 at 4:57 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 16/02/2011 11:24 PM, oguz gurbulak wrote: *Dear All*, I want to generate some initial crystalline structures of my target molecules for md simulations. *Are there any

[gmx-users] free energy blank dgdl

Hello Justin Thanks for your attention. Just to remind you: I am getting blank dgdl and I found this in log file: There are 0 atoms and 0 charges for free energy perturbation EM grompp -f em-l0.mdp -c *.gro -p PE60-0c-itp.top -o em-l0.tpr

Re: [gmx-users] free energy blank dgdl

Moeed wrote: Hello Justin Thanks for your attention. Just to remind you: I am getting blank dgdl and I found this in log file: There are 0 atoms and 0 charges for free energy perturbation EM grompp -f em-l0.mdp -c *.gro -p PE60-0c-itp.top -o

Re: [gmx-users] free energy blank dgdl

hi It seems that your couple-moltype is missing, that is, no molecules will be turned off interaction. dawei On Thu, Feb 17, 2011 at 8:26 AM, Moeed lecie...@googlemail.com wrote: Hello Justin Thanks for your attention. Just to remind you: I am getting blank dgdl and I found this in log

Re: [gmx-users] mismatch between energies of sequential minimization runs

On 17/02/2011 6:47 PM, Efrat Noy wrote: Hi, I am running 2 sequential minimizations with the same mdp file. As expected the second minimization stops in step zero and the resulting structures of the 2 minimization runs are identical (RMSD=0.0). But, the energies of the last step of the first

[gmx-users] Influence of rtpi on chemical potential

Hi I am relatively new to gromacs and molecular dynamics simulations. I am trying to simulate a system of 1000 Argon atoms in an NVT ensemble in a cubic box of size 18.7886 nm(density 10kg/m^3) and temperature 90K. To do this, I have assumed that Argon interacts by Lenard-Jones(12-6)

[gmx-users] domain decomposition error

Hello Justin, I am running in parallel but this error comes up with 8, 7, 6, 5, 4 and even 3 number of processors. I read about domain decomposition on the website and tried less number of processors, as just mentioned. My understanting after reading about the error is that parallel simulation is

Re: [gmx-users] domain decomposition error

Moeed wrote: Hello Justin, I am running in parallel but this error comes up with 8, 7, 6, 5, 4 and even 3 number of processors. I read about domain decomposition on the website and tried less number of processors, as just mentioned. My understanting after reading about the error is that

[gmx-users] I need ligand topology file

Hello everyone, I am using gromacs 4.5 version. I am from cadila healthcare ltd. I have protein with ligand file. But I can't submit prodrg server bcoz this confidancial data. I want to genrate .itp without using prodrg server. Have any way that i can genrate .itp file. Plz help me out. --

Re: [gmx-users] I need ligand topology file

ajanihar...@gmail.com wrote: Hello everyone, I am using gromacs 4.5 version. I am from cadila healthcare ltd. I have protein with ligand file. But I can't submit prodrg server bcoz this confidancial data. I want to genrate .itp without using prodrg server. Have any way that i can genrate

[gmx-users] Re: angle constrain, constrained PF6 anion

Hey, Gyorgy - The problem is definitely with the incorrectly defined constraints as I mentioned yesterday. You may find Chapter 5 of the gromacs manual useful to repair this. I hope to be able to look through your attached system on the weekend, if you don't locate the problem before yourself...

[gmx-users] Weeks Chandler Andersen potential

Hi all,  I want to simulate something and want to use Weeks Chandler Andersen potential.  http://matdl.org/matdlwiki/index.php/softmatter:Weeks-Chandler-Andersen_Potential (http://matdl.org/matdlwiki/index.php/softmatter:Weeks-Chandler-Andersen_Potential) Is table option the only way to go ? 

Re: [gmx-users] Weeks Chandler Andersen potential

Rohit Malshe wrote: Hi all, I want to simulate something and want to use Weeks Chandler Andersen potential. http://matdl.org/matdlwiki/index.php/softmatter:Weeks-Chandler-Andersen_Potential http://matdl.org/matdlwiki/index.php/softmatter:Weeks-Chandler-Andersen_Potential Is table option

[gmx-users] saving velocities and coordinates frequently

Hi , I wish to save velocities and coordinates every step for my system. For saving disk space i dont want to save water molecules. How can i do this ? Amit -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] saving velocities and coordinates frequently

Amit Choubey wrote: Hi , I wish to save velocities and coordinates every step for my system. For saving disk space i dont want to save water molecules. How can i do this ? There is no such option for writing to .trr files, only .xtc files, which do not contain velocities. Implicit

Re: [gmx-users] RE: simulation of a metal binding sites

Thankx for the reply ... Can you refer some papers which can be helpful for me to do MD simulation of proteins with ions ... It will be of great help.. I searched the gromacs user list but couldn't get much material.. On Thu, Feb 17, 2011 at 12:32 AM, Ran Friedman ran.fried...@lnu.se wrote:

Re: [gmx-users] RE: simulation of a metal binding sites

bharat gupta wrote: Thankx for the reply ... Can you refer some papers which can be helpful for me to do MD simulation of proteins with ions ... It will be of great help.. I searched the gromacs user list but couldn't get much material.. This list and its users should not supplant your

[gmx-users] about -CN triple bond

Hi, I am dealing with the lipid bilayer permeation simulation. Most compounds can be finished, but the compounds with CN can't be performed simulation. I have searched the discussion in the gmx-users discussion. The vsite has been mentioned, and I have refered to the gromacs manual. But I don't

[gmx-users] backbone_few_sidechain_fixed

Dear All My protein complex has three chains A B C. I created three posre.itp for backbone and some side chain which is not on the interface for each of the chain. I put these in .top file as follows ; File 'complex.top' was generated ; By user: shahid (511) ; On host:

Re: [gmx-users] backbone_few_sidechain_fixed

On 18/02/2011 5:14 PM, shahid nayeem wrote: Dear All My protein complex has three chains A B C. I created three posre.itp for backbone and some side chain which is not on the interface for each of the chain. I put these in .top file as follows ; File 'complex.top' was generated ;

Re: [gmx-users] saving velocities and coordinates frequently

On 18/02/2011 12:21 PM, Amit Choubey wrote: Hi , I wish to save velocities and coordinates every step for my system. For saving disk space i dont want to save water molecules. How can i do this ? See www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume Mark -- gmx-users

Re: [gmx-users] about -CN triple bond

On 18/02/2011 1:13 PM, C.Y. Chang wrote: Hi, I am dealing with the lipid bilayer permeation simulation. Most compounds can be finished, but the compounds with CN can't be performed simulation. I have searched the discussion in the gmx-users discussion. The vsite has been mentioned, and I have

Re: [gmx-users] RE: simulation of a metal binding sites

Hi, As mentioned by others, there's really lots of literature out there. I thought I mention a recent study we carried out, because it actually helped discover some new ion binding sites based on MD. By re-examining crystal structures based on these results, we could even find experimental

Re: [gmx-users] RE: simulation of a metal binding sites

Thanks for these two references ... I am trying to simulate a zinc ion (Zn++) binding domains .. Actually the study involves grafting the Zinc ion domain onto some other protein to check whether it binds to ions or not and what will be the effect of ion binding onto the topology of the other