Re: [gmx-users] itp file for trehalose

You can refer to following papers: HALVOR S. HANSEN, PHILIPPE H. HÜNENBERGER , JComput Chem 32: 998?1032, 2011 and ? ROBERTO D. LINS, PHILIPPE H. HUNENBERGER. J Comput Chem 26: 1400 ?1412, 2005 Nisha Quoting ABEL Stephane 175950 stephane.a...@cea.fr:

Re: [gmx-users] sugar force fields

Here are few papers you can refer to: Gromos forcefield for hexopyronase-based carbohydrates - Roberto D.Lins and Philippe H. Hunenberger 2005 (In gromos forcefield there are parameters for galactose) An improved OPLS?AA force field for carbohydrates- D Kony 2002 Hope it helps!

Re: [gmx-users] oligoglycines

Thanks Tsjerk! Looks like it is working! Quoting Tsjerk Wassenaar tsje...@gmail.com: Hi Nisha, For building you can also use pymol if you have it installed. On the command line you can issue: pymol -qcd 'editor.build_peptide(GGG);cmd.save(triglycine.pdb,not hydro)' Hope it helps,

[gmx-users] oligoglycines

Hello, I want to simulate n-glycines (diglycine, triglycine..etc) I tried to get the structure from PRODRG, but the program adds H's on the N-terminal instead of on C- terminal. Is there another program I could use, or a site where I could get the structure of oligoglycines? For

Re: [gmx-users] oligoglycines

Thanks Justin! Nisha P Quoting Justin A. Lemkul jalem...@vt.edu: nishap.pa...@utoronto.ca wrote: Hello, I want to simulate n-glycines (diglycine, triglycine..etc) I tried to get the structure from PRODRG, but the program adds H's on the N-terminal instead of on C- terminal. Is

Re: [gmx-users] Carbohydrate simulation: problem with the terminal atoms

I am not sure if you have looked through this paper, but it gives the parameters for sugars. A new GROMOS force field for hexopyranose-based carbohydrates by RD Lins, 2005 A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force?field parameter sets

Re: [gmx-users] Nucleosides OPLS-AA

I apologize, but I am trying to simulate Cytidine (not cytosine). The parameters are given for cytosine. Nisha Quoting David van der Spoel sp...@xray.bmc.uu.se: On 2011-03-18 20.14, nishap.pa...@utoronto.ca wrote: Hello, I am trying to use OPLS-AA force field for simulating nucleosides

Re: [gmx-users] Nucleosides OPLS-AA

I know and I apologize, I mistyped. It is an isolated molecule. I did try to combine the parameters of OPLSAA of carbohydrates(Jorgensen, 1997) with the nucleotide base paper (Jorgensen, 1991). However, I am not sure the partial charge that I should use on the Carbon (C) atom of the sugar

Re: [gmx-users] oplsaa galactose

Hi, I am trying to simulate hexopyronase using OPLS-AA forcefield using parameters from the paper: An improved OPLS?AA force field for carbohydrates, 2002 by Gunsteren. The set of torsional angle parameters in the paper are given in Kcal/mol, but because I am using OPLS-AA I would need

[gmx-users] oplsaa galactose

Hello, I am trying to simulate hexopyronase using OPLS-AA forcefield using parameters from the paper: An improved OPLS?AA force field for carbohydrates, 2002 by Gunsteren. I was looking through the ffoplsaabon.itp file and there are some dihedral parameters for hexopyronase. I am not

Re: [gmx-users] oplsaa galactose

Thanks Justin! Quoting Justin A. Lemkul jalem...@vt.edu: nishap.pa...@utoronto.ca wrote: Hello, I am trying to simulate hexopyronase using OPLS-AA forcefield using parameters from the paper: An improved OPLS?AA force field for carbohydrates, 2002 by Gunsteren. I was looking

[gmx-users] galactose bond stretch

Hello, I ran a simulation of one molecule of galactose (cyclic) in water. After the simulation run, when I checked the trajectory file in VMD, the bonds in the galactose molecule stretched and during the run changed back to its original starting form. I am using GROMOS force field

Re: [gmx-users] galactose bond stretch

Thanks Justin! I am using constraints, but like you said it could be just PBC. I did compare some of my calculations to experimental values and they are fairly similar. Nisha P Quoting Justin A. Lemkul jalem...@vt.edu: nishap.pa...@utoronto.ca wrote: Hello, I ran a

[gmx-users] galactose

Hello, I am trying to simulate galactose in water using Gromos FFG53A6 force field. The molecular formula for galactose is C6H12O6, however in the FFG53A6.rtp file, the molecular formula is C6H10O5 for galactose-A and B. Why is it different? I would really appreciate some help!

[gmx-users] galactose

Hello, I am trying to simulate galactose in water using Gromos FFG53A6 force field. The molecular formula for galactose is C6H12O6, however in the FFG53A6.rtp file, the molecular formula is C6H10O5 for galactose-A and B. Why is it different? I would really appreciate some help!

Re: [gmx-users] galactose

Thanks. I am going to look over it. But I was wondering is it possible to just simulate one molecule of sucrose (glucose+fructose) in water using any of the force fields by Gromacs? I realize I would have to add the parameters to the .rtp files, but as you mentioned that the force fields

[gmx-users] Energy-groups?

Hello, I want to plot the interaction potential energy between my solute and solvent. In my .mdp file I did not mention anything under energygrps,so I am thinking it calculates the energies for the whole system. But is there a way I can extract say for example LJ-14 term between my

Re: [gmx-users] Energy-groups?

Quoting Justin A. Lemkul jalem...@vt.edu: Thanks Justin! I do want the non-bonded potential between my solute and solvent. So in my .mdp file I put my solute and solvent as energygrps and ran mdrun using this command: mdrun -s md1.tpr(including energygrps) -rerun md.xtc (my trajectory)

Re: [gmx-users] Energy-groups?

I see. It did work . Thanks a lot Justin! Quoting Justin A. Lemkul jalem...@vt.edu: nishap.pa...@utoronto.ca wrote: Quoting Justin A. Lemkul jalem...@vt.edu: Thanks Justin! I do want the non-bonded potential between my solute and solvent. So in my .mdp file I put my solute and solvent

[gmx-users] LJ Plot

Hello, Is there an option to plot Lennard Jones potential? I tried looking through the list and manual but I did not find any suggestions on how I could plot a LJ 6-12 potential plot. Nisha -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] LJ Plot

Quoting Justin A. Lemkul jalem...@vt.edu: How does sigeps read the input file? I tried using sigeps to plot LJ for different solutes in solvent and it gives me the same C6 and C12 value, when it runs, which seems a weird. c6= 1.0e-03, c12= 1.0e-06 sigma = 0.0,

Re: [gmx-users] LJ Plot

Quoting Justin A. Lemkul jalem...@vt.edu: I actually want to plot my simulation with ad without the attractive term C6 of van der Waals and superimpose them to see the difference. nishap.pa...@utoronto.ca wrote: Quoting Justin A. Lemkul jalem...@vt.edu: How does sigeps read the input

Re: [gmx-users] LJ Plot

Quoting ms deviceran...@gmail.com: I did two different simulation. One with van der Waals attractive term and one without van der Waals attractive term. And so to see the difference between the LJ potential between the two simulation I wanted to plot the LJ potential for both the

Re: [gmx-users] C6 attractive term off OPLSAA

I ran the simulation using a different force field ffG53a6. I modified the ffG53a6nb.itp file by changing the term C6 to zero for nonbonded parameters, but this time for urea in water. The simulation ran fine without any warning or exploding. I don't understand why it would work with one

Re: [gmx-users] C6 attractive term off OPLSAA

I see. I actually want to compare my RDFs with C6 term off. Earlier I tried using force.c code file and turned C6 = 0, but when i compared my RDFs, it didn't look any different so I am not sure if it even worked at all or made any difference to the simulation, but again I was using OPLS-AA

RE: [gmx-users] C6 attractive term off OPLSAA

I am going to give that a try. Thanks. Quoting Berk Hess g...@hotmail.com: Hi, Maybe it is not so clear from the topology table in the manual, but when you supply sigma and epsilon as non-bonded parameters, as for OPLS, the nonbond_params section also expects sigma and epsilon. So it

[gmx-users] RE:C6 attractive term off OPLSAA

Would I change the sigma to negative in my nb.itp file the way it is set or do I need to include a [nonbond_params] section and make sigma negative in that specific section? because I realize from the manual OPLS-AA uses combination rule 3 but in the manual it shows to combine sigma for i

Re: [gmx-users] C6 attractive term off OPLSAA

I tried using the nonbonded parameters as defined below in my ffoplsaanb.itp file for methanol in water and this is the syntax I used: [nonbond_params ] ;i j funcc6 c12 opls_154opls_111 1 0.00E+000 2.43E-006 opls_154opls_112 1 0.00E+000

[gmx-users] C6 attractive term off OPLSAA

Hello, I have a concern regarding C6 attractive term in LJ potential. I am using OPLS-AA force field, and I wish to turn off attractive term C6 by setting the parameters to zero. One of the suggestion was to add a [nonbond_params] in my ffoplsaanb.itp file and set the C6 to zero

Re: [gmx-users] C6 attractive term off OPLSAA

Okay I am going to give it a try. I just wanted to make sure I was calculating C6 and C12 correctly as well using sigma and epsilon according to rule 3 C12 = Sigma^(6)*C6 C6 = 4*sigma^(6)*epsilon Thanks Quoting Justin A. Lemkul jalem...@vt.edu: nishap.pa...@utoronto.ca wrote: Hello,

Re: [gmx-users] electrostatic interaction

Hello, It doesn't contribute as such. I was using a different force field before OPLSAA and it was all atom so I could make the charges zero in the topology file, I wanted to do the same. Quoting Justin A. Lemkul jalem...@vt.edu: Mark Abraham wrote: On 16/11/2010 7:14 AM,

[gmx-users] electrostatic interaction

Hello, I want to turn off electrostatic interactions between CH4 and SOL in my system. I am using ffG53a6 forcefield for CH4 and spc for my water model. CH4 is an united atom and so I can't make the charges zero in the topology. Is there any other way I can turn off electrostatic

[gmx-users] LJ potential

Hello, Is there a way to turn off the 6-term in LJ 6-12 potential? -Nisha P. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't

Re: [gmx-users] LJ potential

How can I do that using OPLSAA, because in the nb.itp file the values are for sigma/epsilon? Can I change C6=0 in the code file? Quoting David van der Spoel sp...@xray.bmc.uu.se: On 2010-09-27 18.37, nishap.pa...@utoronto.ca wrote: Hello, Is there a way to turn off the 6-term in LJ 6-12

[gmx-users] Urea-water

Hello, I am simulating 2M urea in water with single methane (77 urea + 1926 water). I used genbox -ci -nmol to add the number of urea molecules and then used genbox to add water molecules (as suggested in the manual). When I tried to do energy minimization this is what I got :

Re: [gmx-users] Urea-water

I did look at the plot, and it shows that the curve is smoothing right under zero at -1.00e+05 but then why does the average potential show a positive number? Shouldn't that number be negative as well? Quoting David van der Spoel sp...@xray.bmc.uu.se: On 2010-09-20 19.58,

[gmx-users] NAGA

Hello, I am trying to simulate N-methylglycine amide. I selected 'none' for the termini using oplsaa forcefield. I got the topology but I got the error saying: ERROR 1 [file topol.top, line 126]: No default Ryckaert-Bell. types I checked the line 126 in my topol file and it is the

[gmx-users] VDWradii.dat

Hello, I have a question about how gromacs assigns VDW radii for ions. I checked the vdwradii.dat file but it does not mention any ions, so where do the parameters for ions come from? I got the .pqr file for sodium and I got the atomic radii of 1.6652A, I am not sure where that value

Re: [gmx-users] VDWradii.dat

I did use this command: editconf -f md.tpr -mead na.pqr. If I understand it correctly for -sig56 option, I would use the min rvdw from my mdp and divide it by 2 and use that value in the command line? Quoting David van der Spoel sp...@xray.bmc.uu.se: On 2010-08-30 20.32,

Re: [gmx-users] VDWradii.dat

Also, I am using OPLS-AA force field with TIP3P water Quoting David van der Spoel sp...@xray.bmc.uu.se: On 2010-08-30 20.32, nishap.pa...@utoronto.ca wrote: Hello, I have a question about how gromacs assigns VDW radii for ions. I checked the vdwradii.dat file but it does not mention any

Re: [gmx-users] VDWradii.dat

Okay I see what you mean. Thanks alot! Quoting Justin A. Lemkul jalem...@vt.edu: nishap.pa...@utoronto.ca wrote: I did use this command: editconf -f md.tpr -mead na.pqr. If I understand it correctly for -sig56 option, I would use the min rvdw from my mdp and divide it by 2 and use

Re: [gmx-users] VDW radii of Br and K+

Thanks! I did overlook that. Quoting David van der Spoel sp...@xray.bmc.uu.se: On 2010-08-24 22.53, nishap.pa...@utoronto.ca wrote: Hello, I converted a .tpr file for Bromine ion and Potassium ion using -mead option and editconf. It gives out the Van der Waals radius of the atom, but I

[gmx-users] VDW radii of Br and K+

Hello, I converted a .tpr file for Bromine ion and Potassium ion using -mead option and editconf. It gives out the Van der Waals radius of the atom, but I don't understand why i got ~2.46A for Potassium and ~2.31A for Bromide. Isn't the bromide ion bigger than Potassium? And I used

[gmx-users] NaCl

Hello, I want to simulate a simple NaCl ion in water. I know the method using genion which adds individual Na+ and Cl- ion, but I wish to simulate Na-Cl connected rather than free ions floating in water. When I ran the grompp command I got the error: No default Bond types So I am

Re: [gmx-users] NaCl

I believe the bonds are not defined in the OPLS-AA force field for NaCl. I know this might sound like a stupid question, but is there a way to determine the bond force constant (kb), I tried to look it up, but I couldn't find anything. Quoting Justin A. Lemkul jalem...@vt.edu:

Re: [gmx-users] Conformational sampling

Thanks. I am definitely going to look into that. Quoting chris.ne...@utoronto.ca: Nisha: Simply applying available tools and seeing if the distribution looks okay is not a good plan. You should have a very well-defined idea of what you are trying to test and then pick a tool to get that

Re: [gmx-users] Conformational sampling

Okay so I tried to analyze the torsion using g_chi and g_rama for one glycine zwitterion in water. for g_rama I didn't see anything in xmgrace, and same for g_chi. I used this command for g_chi g_chi -f traj.xtc -s gly.gro -phi -psi When I run the command it says 1 residue with dihedrals

Re: [gmx-users] Conformational sampling

So is there a way I can test for convergence for my zwitterion for 100ns run? Quoting Justin A. Lemkul jalem...@vt.edu: nishap.pa...@utoronto.ca wrote: Okay so I tried to analyze the torsion using g_chi and g_rama for one glycine zwitterion in water. for g_rama I didn't see anything

Re: [gmx-users] Conformational sampling

Well I guess, what I am trying to get at is, for my system I want to make sure that 100ns has covered all the conformational changes within the molecule, although I know there is not that much conformational changes for glycine molecule, but I just wanted to confirm. I did run g_angle

[gmx-users] Conformational sampling

Hello, I would like to do conformational sampling for my simulation of one glycine in its zwitterionic form in water and obtain a PMF curve to see if the system is equilibrated and that all possible torsions are covered for my 100ns run. I am not sure how to approach this issue. Is

[gmx-users] combining replicate xtc files

Hello, I ran a simulation for 100ns on 2 nodes (16 cores). I tried to generate replicates with different starting trajectories and ran it on one core, so basically I have 64 replicates with different starting trajectories and I am using 8 nodes. I wish to combine all the .xtc files

Re: [gmx-users] Domain decomposition error

Thanks Mark, I did play around with the -npme option a little and turns out using -npme 1 works for the system this is mdrun command I have in the script file mdrun_openmpi -nosum -dlb yes -npme 1 -cpt 40 -maxh 48 -deffnm md Thanks. Quoting Mark Abraham mark.abra...@anu.edu.au: -

[gmx-users] Domain decomposition error

Hello, I got this following error when I was trying to run a simulation of ethanol-water box size 4*4*4 nm (~6530 atoms). Fatal error: There is no domain decomposition for 14 nodes that is compatible with the given box and a minimum cell size of 0.62175 nm Change the number of nodes or

Re: [gmx-users] Domain decomposition error

Thanks Justin. But how come it worked for methanol. The system is of the same size , and all the parameters are same, so I don't understand why it won't work for ethanol. Quoting Justin A. Lemkul jalem...@vt.edu: nishap.pa...@utoronto.ca wrote: Hello, I got this following error when

[gmx-users] trjcat settime

Hello, I have a concern regarding what -settime actually does. I ran replicates of same simulation with different starting trajectories, basically to get more sampling. Now I wish to combine all the .xtc files from each replicates so I can analyze it as a whole. Now what's the

[gmx-users] Hard Sphere?

Hello, I am not sure if anyone else has some experience with this, but I want to simulate a hard sphere in a solvent (water and heptane). I believe for the hard spheres, the attractive terms for LJ potential is very negligible so the only term to take into account is repulsion, from

[gmx-users] Magic error xtc?

Hello, I am running simulations and I got Magic Number error: Fatal error: Magic Number Error in XTC file (read 0, should be 1995) Checking file md.part0002.xtc Reading frame 0 time 48190.004 # Atoms 6533 Precision 0.001 (nm) Reading frame 178000 time 83790.008 Part one of the

Re: [gmx-users] Magic error xtc?

Hi Justin, Well the way I continued my second part of the simulation was using my md.cpt file. I checked my .cpt file and this is what I got: Last frame -1 time 83786.961 , so I guess my second run updated the file, so does this mean I have to do the whole simulation again? or

Re: [gmx-users] Magic error xtc?

I am trying using prev_md.cpt file. I checked and it looks okay, so hopefully it will work. If not I will try using .trr files. Thanks Quoting Tsjerk Wassenaar tsje...@gmail.com: Hey, Otherwise it's also still possible to do old style continuation with a frame from the .trr/.edr file,

[gmx-users] combining energy files

Hello, I am a running a simulation of 100ns, so I have two edr files md.edr and md.part0002.edr. When I calculate some of the energy values using g_energy for each of the .edr files individually I get the following result: For md.edr: Statistics over 27120401 steps [ 0. thru

Re: [gmx-users] combining energy files

I am using gromacs-4.0.5. Thanks. Quoting XAvier Periole x.peri...@rug.nl: That looks like a nice bug! You should specify which gmx version you are using. That would help getting it fixed. On Apr 13, 2010, at 21:34, nishap.pa...@utoronto.ca wrote: Hello, I am a running a simulation of

Re: [gmx-users] density tip3p

Hi Zuzana, You are right. I did get my density to ~0.986g/cm3, and I actually came across this other paper by Price and Brooks, and initially they get a density of Tip3p using pme at around 0.979g/cm3, but they tweak some of the parameters in oplsaa to get the correct density. I am

Re: [gmx-users] density tip3p

Hello, So I looked at the manual and I changed my mdp parameters as follows to equilibrate at a constant pressure. RUN CONTROL PARAMETERS = integrator = sd tinit= 0 dt = 0.002 nsteps = 50 nstcomm

[gmx-users] Pressure average problem

Hello, I am simulating a box of water (TIP3P ) in a box of 3nm*3*3nm.My simulations are 100ns each. I am using different cut-off. i.e vdw-type = switch rvdw-switch = 0.8 rvdw = 1.0, 1.2 and 1.3 and these are my parameters for Pressure

Re: [gmx-users] Pressure average problem

Quoting Mark Abraham mark.abra...@anu.edu.au: On 31/03/2010 5:19 AM, nishap.pa...@utoronto.ca wrote: Hello, I am simulating a box of water (TIP3P ) in a box of 3nm*3*3nm.My simulations are 100ns each. I am using different cut-off. i.e vdw-type = switch rvdw-switch = 0.8 rvdw = 1.0, 1.2 and

[gmx-users] density tip3p

I have a box (3x3x3nm) of Tip3p water molecules ~900 and the density when I create the box using genbox is 997.177g/l. I did energy minimization run and the potential energy did converge smoothly, so I did NPT equilibration run of 100ps and I got the density value of 975g/l. Why does the

Re: [gmx-users] density tip3p

Thanks. I will look up the manual again. Quoting Sander Pronk pr...@cbr.su.se: Hi Nisha, Looking at your .mdp, there are some issues that might lead to the behavior that you describe: First: you should try to look up the published densities for tip3p water at 300K - they might actually

Re: [gmx-users] Re: density vs time

What do you mean the value for methane? As in the charges? This is my topology file and I am using OPLS-AA for methane. Include forcefield parameters #include ffoplsaa.itp [ moleculetype ] ; Namenrexcl Methane3 [ atoms ] ; nr type resnr residue atom cgnr

[gmx-users] density vs time

Hello, I am simulating one methane molecule in 899 water molecues in the box size of 3 3 3 nm (27nm^3). I would like to determine density vs time. Is there a way I can do that? I am running my simulation at constant Volume i.e. no pressure coupling. I tried using g_density but it

Re: [gmx-users] density vs time

I am trying to get an rdf graph actually, and my values are very close to one, but not exactly one, and I was wondering if there is some normalization issue with g_rdf? These are my values for rdf: 0 0 0.002 0 0.004 0 0.006 0 0.008

[gmx-users] waterbox

Hello, I am trying to use genbox to add water molecules to my system consisting of one molecule of ethane in the box size of 4 4 4nm( 64nm^3). If I understand it correctly, with the system of that size, I should have ~2080 water molecules in my system, but instead genbox adds ~2177

Re: [gmx-users] waterbox

Hi Justin, Well from the previous post: The number density for water should be about 32.5 waters per cubic nanometer. So if my box size is 4 4 4 =64nm^3, then shouldn't number of water molecules be 64*32.5 = 2080? May be I am not understanding it correctly. I am using Tip3p water

Re: [gmx-users] ethanol bond types

Quoting David van der Spoel sp...@xray.bmc.uu.se: On 3/3/10 8:14 PM, nishap.pa...@utoronto.ca wrote: Hello, I am trying to simulate Ethanol in water using OPLSAA. I already tried it with all atoms, but now I want to try it with United atoms for ethanol, i.e. CH3,CH2,OH, and HO in my

[gmx-users] ethanol bond types

Hello, I am trying to simulate Ethanol in water using OPLSAA. I already tried it with all atoms, but now I want to try it with United atoms for ethanol, i.e. CH3,CH2,OH, and HO in my topology file. I created the topology but I got an error saying 'No bond types', so I checked

[gmx-users] extending simulation confusion?

Hi, I am trying to extend my simulation time from 100ns - 300ns. So I used the command : tpbconv -s old.tpr -extend 10 -o new.tpr but I got this: Extending remaining runtime of by 20 ps (now 14992 steps) Writing statusfile with starting step 0 and length 14992

Re: [gmx-users] rdf

Hi Will, I have been using pme from the very start and it didn't help with the volume. Could you please elaborate on what you mean by average g(r) over every molecule? And because my rdf-s are not smooth enough even with 100ns, I get fluctuating data using rdf-s. -Nisha

Re: [gmx-users] rdf

Hi, I saved my rdf plot as a pdf file and I have attached it to this email. Hopefully it will work. My system is one methane with 893 molecules of tip3p water in a cubic box of size 3 3 3 (nm). My topology file is : ; Include forcefield parameters #include ffoplsaa.itp [ moleculetype

Re: [gmx-users] rdf

okay this should work http://docs.google.com/fileview?id=0B_QNmYARywUiNzE0MDA0NWMtYjFiMy00MTRjLThkNDMtNTk3NDgyNjcxZTgxhl=en -Nisha Quoting chris.ne...@utoronto.ca: I didn't get the attachment. Please upload the image to some website and post the link. --original message -- I saved my

[gmx-users] rdf

Hi, I am doing rdf's of simple molecules. I ran my simulation of water and methane for 100ns to get a smoother curve for the rdf. I am trying to determine the volume, and after a certain cut-off I would assume my values to be constant (i.e. volume), but the values fluctuate alot (i.e.

[gmx-users] methane in water

Hello, I am running rdf simulations, and I tried running simple methane using OPLS-AA force-field for 100ns. I was hoping to get a smoother curve for such a small molecule in 100ns. Could someone please look over my mdp parameters and suggest if I am missing something. Thanks. Nisha

[gmx-users] cut-off

Hello, I wanted to know, if say my box is 30A (cubic) and if I set my cut-off lengths i.e. rvdw-switch = 0.8 and rvdw =0.9 , does that mean, the simulation will cut-0ff at 9A? Should I be changing that to 1.5nm (to get half the box cut-off)? I am a little confused about that. Thanks.

Re: [gmx-users] cut-off

I see what you mean, so say if I am doing RDF, the values beyond 9A would be bogus? Quoting Justin A. Lemkul jalem...@vt.edu: nishap.pa...@utoronto.ca wrote: Hello, I wanted to know, if say my box is 30A (cubic) and if I set my cut-off lengths i.e. rvdw-switch = 0.8 and rvdw =0.9

[gmx-users] Ammonia in Water

Hello, I created a topology file for 1 ammonia in water. Could someone please have a look at the file and let me know if it looks okay. Thanks Nisha Patel ; Include forcefield parameters #include ffoplsaa.itp [ moleculetype ] ; Namenrexcl Ammonia 3 [ atoms ] ;

[gmx-users] Error during minimization

I have a question regarding the simulations that I am running. I tried creating a pdb file with one methane and water molecules, but the system keeps showing 'bad contact' error when I run the minimization step and I don't understand what I am doing wrong. This is my methane file : TITLE

[gmx-users] Helpful Information Energy Minimization errors

Hello gmx users, After running energy minimization steps, I got the following error: teepest Descents: Tolerance (Fmax) = 1.0e+00 Number of steps= 100 Step=0, Dmax= 1.0e-02 nm, Epot= -2.84750e+04 Fmax= 1.53401e+04, atom= 2501 Step=1, Dmax= 1.0e-02 nm,

[gmx-users] pdb file for ammonia

Does anyone know where I can get a pdb file for ammonia? I tried searching but I am not sure if there is a website for the pdb files I can use in gromac. Any suggestions would be helpful. Thanks. Nisha -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Check for bad contacts and/or reduce the timestep

Hi, I tried energy minimization and I am getting the error while I am running the minimization step. But then I still tried to carry on with normal md-simulation, and it was fine, but I am sure it won't give me the result that it should. Is there a reason for that? I have tried very low

Re: [gmx-users] Check for bad contacts and/or reduce the timestep

Hi Justin, I am trying to plot rdf of one methane molecule in water (spc water, 1095(water molecule in my file). I did create the file using genbox (31.010 31.010 31.010). This is the energy minimization file I am using: title = Methane in water cpp = /lib/cpp

Re: [gmx-users] Check for bad contacts and/or reduce the timestep

Hi, You are right, I had to delete some water molecules, it is working fine now. Thanks. -Nisha P Quoting Justin A. Lemkul jalem...@vt.edu: nishap.pa...@utoronto.ca wrote: Hi Justin, I am trying to plot rdf of one methane molecule in water (spc water, 1095(water molecule in my

[gmx-users] RDF methanol and water

HI, Okay, so I am trying to plot rdf of one methanol this time in water. Is there a way to select methanol molecule as a whole (i.e. get rdf from the center of the molecule), instead of Me, O and H. Even though I put Me, O and H in same group, I am getting a weird rdf plot (Attached to

[gmx-users] Check for bad contacts and/or reduce the timestep

Hi, I am trying to run a simulation with 1360 Tip4p water molecules and one methane molecule (Box size: 35.500 35.3371 35.500 and Total 5541 atoms) but I am getting the error: t = 0.000 ps: Water molecule starting at atom 5433 can not be settled. Check for bad contacts and/or reduce the

Re: [gmx-users] Check for bad contacts and/or reduce the timestep

- Forwarded message from nishap.pa...@utoronto.ca - Date: Mon, 14 Dec 2009 14:06:30 -0500 From: nishap.pa...@utoronto.ca Reply-To: nishap.pa...@utoronto.ca Subject: Re: [gmx-users] Check for bad contacts and/or reduce the timestep To: Justin A. Lemkul jalem...@vt.edu I