Re: [gmx-users] Does GMX compute coulomb interaction between oxygen and hydrogen in SPC water model?

xuji wrote: > Hi all gromcas users: > > In SPC water model, it only has oxygen-oxygen VDW interactons. > So is it the same with coulomb interatctions? No, otherwise it would be a one-point water model. All SPC water atoms have partial charges - see spc.itp. Mark

[gmx-users] Does GMX compute coulomb interaction between oxygen and hydrogen in SPC water model?

Hi all gromcas users: In SPC water model, it only has oxygen-oxygen VDW interactons. So is it the same with coulomb interatctions? Thanks for any advice in advance! 2009-10-24 Ji Xu The State Key Laboratory of Multiphase Complex System Institute of Process Engineering Chinese Academy of Sci

[gmx-users] Re: Re: how to calculate the vaporation enthalpy of pure small organic compound (David van der Spoel)

Hi David, Thank you for your help. I am very sorry to trouble you. I have know your means that the gas-phase energy should be considered. But I am confused that you said "the gas-phase energy (with com removed) and add kT". What is "the gas-phase energy (with com removed) " and Could you talk abou

Re: [gmx-users] positional restraint

krishnakumar wrote: Hi, I was wondering if it would be possible to apply positional restraint to an atom w.r.t an arbitrary coordinate. Say for eg. I want to constrain the distance between an atom and the origin(0,0,0) during MD. Is it possible to do that in GROMACS. I don't believe t

Re: [gmx-users] Which membrane result is more reliable?

Kirill Bessonov wrote: Hello Justin, You helped me before, and I am grateful for that. So basically my summer research had ended up with the following results: I have included my *.ipt files this message is long. *My question: 1)why once simulation is giving me stable aplha-helix and oth

[gmx-users] Which membrane result is more reliable?

Hello Justin, You helped me before, and I am grateful for that. So basically my summer research had ended up with the following results: I have included my *.ipt files this message is long. *My question: 1)why once simulation is giving me stable aplha-helix and other is not if membranes are sim

[gmx-users] positional restraint

Hi, I was wondering if it would be possible to apply positional restraint to an atom w.r.t an arbitrary coordinate. Say for eg. I want to constrain the distance between an atom and the origin(0,0,0) during MD. Is it possible to do that in GROMACS. Thanks Krishna

Re: [gmx-users] how to stop duplicate atoms from being deleted

Justin A. Lemkul wrote: I can see how this rapidly becomes difficult :) I don't believe that pdb2gmx can handle such "multi-directional" bonding, since the residues that are connected are not necessarily numerically sequential. I should amend this statement (typing quicker than the brain c

Re: [gmx-users] how to stop duplicate atoms from being deleted

Jennifer Williams wrote: Thanks again for the help. I?ve given it a go but am not overly confident or exactly sure how I would translate this method to my system. This is because rather than having a chain with a well defined start and finish I have a giant covalent structure (like a web)

Re: [gmx-users] how to stop duplicate atoms from being deleted

Thanks again for the help. I?ve given it a go but am not overly confident or exactly sure how I would translate this method to my system. This is because rather than having a chain with a well defined start and finish I have a giant covalent structure (like a web) where each silicon is

Re: [gmx-users] How can measure the end-yo end distance of a peptide from the .xtc file

haifeng YUAN wrote: Dear all, I would like to get the distance information of the small peptide chain from the .xtc file, but the g_mindist seems can only get the distance information from one group to another. How I can get the end to end distance? I mean the distance between an en

[gmx-users] How can measure the end-yo end distance of a peptide from the .xtc file

Dear all, I would like to get the distance information of the small peptide chain from the .xtc file, but the g_mindist seems can only get the distance information from one group to another. How I can get the end to end distance? I mean the distance between an end atom of the short c

Re: Fwd: [gmx-users] scripts to generate topology CG

Francesco Pietra wrote: grep W solvated.gro | wc -l and use that number in the topology? I forgot to add that the graphic program uses the above grep command, I don't understand this statement. giving the same number of W as the line command. The number of DCCP is diminished by those de

Re: [gmx-users] scripts to generate topology CG

Francesco Pietra wrote: On Fri, Oct 23, 2009 at 4:14 PM, Justin A. Lemkul wrote: Francesco Pietra wrote: Hello Sunny: I had already generated a valid .itp file for my protein using seq2itp. That .itp works for both the protein itself and the protein graphically inserted into a bilayer. When

Fwd: [gmx-users] scripts to generate topology CG

-- Forwarded message -- From: Francesco Pietra Date: Fri, Oct 23, 2009 at 5:01 PM Subject: Re: [gmx-users] scripts to generate topology CG To: jalem...@vt.edu, Discussion list for GROMACS users On Fri, Oct 23, 2009 at 4:14 PM, Justin A. Lemkul wrote: > > > Francesco Pietra wrot

[gmx-users] Re: Re: how to calculate the vaporation enthalpy of pure small organic compound (Justin A. Lemkul)

Dear Justin, Thank you for your help. I indeed didn't use the option "-nmol 512". > > >Jinyao Wang wrote: >> Hi gmx-users, >> I want to calcualted the the vaporation enthalpy of benzaldehyde >> I think that the the vaporation enthalpy is the sum of non-bond interacion >> among the benzalde

Re: [gmx-users] scripts to generate topology CG

On Fri, Oct 23, 2009 at 4:14 PM, Justin A. Lemkul wrote: > > > Francesco Pietra wrote: >> >> Hello Sunny: >> I had already generated a valid .itp file for my protein using >> seq2itp. That .itp works for both the protein itself and the protein >> graphically inserted into a bilayer. When I add gra

Re: [gmx-users] how to calculate the vaporation enthalpy of pure small organic compound

Justin A. Lemkul wrote: Jinyao Wang wrote: Hi gmx-users, I want to calcualted the the vaporation enthalpy of benzaldehyde I think that the the vaporation enthalpy is the sum of non-bond interacion among the benzaldehyde molecule.So I made a NPT system simulation including 512 benzald

Re: [gmx-users] how to calculate the vaporation enthalpy of pure small organic compound

Jinyao Wang wrote: Hi gmx-users, I want to calcualted the the vaporation enthalpy of benzaldehyde I think that the the vaporation enthalpy is the sum of non-bond interacion among the benzaldehyde molecule. So I made a NPT system simulation including 512 benzaldehyde molecule. The foll

[gmx-users] how to calculate the vaporation enthalpy of pure small organic compound

Hi gmx-users, I want to calcualted the the vaporation enthalpy of benzaldehyde I think that the the vaporation enthalpy is the sum of non-bond interacion among the benzaldehyde molecule. So I made a NPT system simulation including 512 benzaldehyde molecule. The following is the intermole

Re: [gmx-users] scripts to generate topology CG

Francesco Pietra wrote: Hello Sunny: I had already generated a valid .itp file for my protein using seq2itp. That .itp works for both the protein itself and the protein graphically inserted into a bilayer. When I add graphically further water it does not work any more. I thought there is someth

Re: [gmx-users] scripts to generate topology CG

Hello Sunny: I had already generated a valid .itp file for my protein using seq2itp. That .itp works for both the protein itself and the protein graphically inserted into a bilayer. When I add graphically further water it does not work any more. I thought there is something else that manages water

Re: [gmx-users] how to stop duplicate atoms from being deleted

Jennifer Williams wrote: Hi Justin, Thanks for the reply. I am in fact studying one huge molecule. All of my atoms are bonded together in one large structure (kind of like a zeolite) so I have necessarily defined them as a single residue. I would argue that you have a polymer, which can

Re: [gmx-users] how to stop duplicate atoms from being deleted

Hi Justin, Thanks for the reply. I am in fact studying one huge molecule. All of my atoms are bonded together in one large structure (kind of like a zeolite) so I have necessarily defined them as a single residue. There is no way I can split this molecule into smaller subunits and thus d

Re: [gmx-users] Re: Chloroform (CHCl3) solvent box for G53a5 force field

Pablo Englebienne wrote: Following up on the previous message, I noticed that the topology I previously sent (including 10 bonds) works for a minimization, but not for an MD simulation. grompp issues the following warning: WARNING 1 [file topol.top, line 29]: Molecule type 'CHCL3' has 10 co

Re: [gmx-users] how to stop duplicate atoms from being deleted

Quoting Jennifer Williams : > > Hello > > I am studying a mesoporous silica for which there is no topology in > gromacs-to try to automate the process of generating a topology file > (x2top doesn?t work), I am using pdb2gmx (or rather trying to). > > I have parameters for my silica structure and h

[gmx-users] how to stop duplicate atoms from being deleted

Hello I am studying a mesoporous silica for which there is no topology in gromacs-to try to automate the process of generating a topology file (x2top doesn?t work), I am using pdb2gmx (or rather trying to). I have parameters for my silica structure and have added a new section for my mol

[gmx-users] Re: Chloroform (CHCl3) solvent box for G53a5 force field

Following up on the previous message, I noticed that the topology I previously sent (including 10 bonds) works for a minimization, but not for an MD simulation. grompp issues the following warning: WARNING 1 [file topol.top, line 29]: Molecule type 'CHCL3' has 10 constraints. For stability an

Re: [gmx-users] POPG-Martini Force Field

On Oct 23, 2009, at 9:45 AM, Amit Choubey wrote: On Fri, Oct 23, 2009 at 12:33 AM, XAvier Periole wrote: On Oct 22, 2009, at 11:28 PM, Amit Choubey wrote: On Thu, Oct 22, 2009 at 9:53 AM, S hv wrote: Hi, I am currently working with peptide/lipids interactions using the martini fo

RE: [gmx-users] Setting up an infinitely hard wall

Hi, If you have a wall potential, you can reweight the configurations with weight 0 if one or more particles are beyond the wall and exp(Vwall/kT) if no particles are beyond the wall. This will only work efficiently if you choose the wall potential in a smart way. I managed to get an efficiency o

Re: [gmx-users] POPG-Martini Force Field

On Fri, Oct 23, 2009 at 12:33 AM, XAvier Periole wrote: > > On Oct 22, 2009, at 11:28 PM, Amit Choubey wrote: > > > > On Thu, Oct 22, 2009 at 9:53 AM, S hv wrote: > >> Hi, >> >> I am currently working with peptide/lipids interactions using the martini >> force field. I want to built a bacterial

Re: [gmx-users] POPG-Martini Force Field

On Oct 22, 2009, at 11:28 PM, Amit Choubey wrote: On Thu, Oct 22, 2009 at 9:53 AM, S hv wrote: Hi, I am currently working with peptide/lipids interactions using the martini force field. I want to built a bacterial membrane, so I trying to find the topology of the POPG lipid but until n

Re: [gmx-users] Setting up an infinitely hard wall

Hi Berk, Thank you for the response. I have obtained distributions with in infinite wall by simulating with an > softer wall > and unbiasing with configurations with the wall potential. > Could you explain the above ? I am not sure if i get your point. > But if you need the dynamics, or you wan

RE: [gmx-users] Setting up an infinitely hard wall

Hi, I have obtained distributions with in infinite wall by simulating with an softer wall and unbiasing with configurations with the wall potential. But if you need the dynamics, or you want less hassle during the simulation, you will have to do a bit more effort in coding an infinitely hard wal