Re: [gmx-users] Charge groups

On 5/13/13 8:23 PM, Marcelo Vanean wrote: Hi. I'm with doubts concerning the charge groups. I am simulating ethylene glycol and the only way of charged groups are neutral is putting all atoms in only one charge group. This is advisable? Is that a problem? What is the greatest number of atoms in

[gmx-users] Charge groups

Hi. I'm with doubts concerning the charge groups. I am simulating ethylene glycol and the only way of charged groups are neutral is putting all atoms in only one charge group. This is advisable? Is that a problem? What is the greatest number of atoms in a charge group which is recommended? -- gmx-

Re: [gmx-users] Charge on the protein

You're modelling a real physical system. You've chosen some ionization states, perhaps implicitly. Do those make sense for what you are modelling? Does a charged system make sense for what you are modelling? Mark On Fri, Jan 25, 2013 at 10:07 AM, wrote: > Hello > > while executing grompp follow

[gmx-users] Charge on the protein

Hello while executing grompp following message is seen although the .tpr file is generated System has non-zero total charge: -3.00 Total charge should normally be an integer I have used AMBER99SB as the force field to prep the topology to run implicit solvent simulation. How relevant

Re: [gmx-users] charge groups

On 11/5/12 9:24 AM, akn wrote: Dear gmx users, I'm using PME for electrostatic interactions and so I don't need to arrange charge groups. I think the treatment of charge groups relies more on the force field rather than the electrostatics method. With PME, it is true that you do not neces

[gmx-users] charge groups

Dear gmx users, I'm using PME for electrostatic interactions and so I don't need to arrange charge groups. I want to learn how should I fill cgnr coloumn if I don't want to arrange charge groups. İf my molecule contains ten atoms, is it enough to write the numbers from 1 to 10 for each atom at the

Re: [gmx-users] charge calculation........

As mentioned, you should make RESP charges for AMBER parameters. ESP parameters are furthermore often a bit bizarre (aliphatic carbons with charge well below -1etc.). Erik 14.11 skrev tarak karmakar: > Thanks Mark. > > I have gone through the link "Parameterization of novel molecules" and > I

Re: [gmx-users] charge calculation........

Thanks Mark. I have gone through the link "Parameterization of novel molecules" and I see quantum calculations can be handy for this type of charge calculation (AMBER). So for the unprotonated tyrosine, I am taking two more amino acids (left and right) and calculating ESP charges of the tri-peptid

[gmx-users] charge calculation........

Hi Since you want to use the AMBER force for your calculations, you will need to compute the RESP charges for your new residue (unprotoned TYR) and add the charges in your *rtp file. To compute the charges, you can use the RED.Server (http://q4md-forcefieldtools.org/REDS/). It is not easy, s

Re: [gmx-users] charge calculation........

On 17/09/2012 10:01 PM, tarak karmakar wrote: Dear All, I want to have one of tyrosine residues in my protein to be unprotonated. I am using amber force field for the simulation. But in aminoacid.rtp there is no entry for the unprotonated one. So I am adding it by myself in to the

[gmx-users] charge calculation........

Dear All, I want to have one of tyrosine residues in my protein to be unprotonated. I am using amber force field for the simulation. But in aminoacid.rtp there is no entry for the unprotonated one. So I am adding it by myself in to the .rtp file. Now I am bit confused with the charge

Re: [gmx-users] Charge Group Number in itp File (cgnr)

On 11/09/2012 7:55 AM, Andrew DeYoung wrote: Hi, In the [ atoms ] section of an .itp file, there is a column (cgnr) where a charge group number is given (an integer). This cgnr column is shown in, for example, the manual version 4.5.4 in Section 5.7. My question is, do the charge group numbers

[gmx-users] Charge Group Number in itp File (cgnr)

Hi, In the [ atoms ] section of an .itp file, there is a column (cgnr) where a charge group number is given (an integer). This cgnr column is shown in, for example, the manual version 4.5.4 in Section 5.7. My question is, do the charge group numbers have to be _consecutive_ integers? For some

Re: [gmx-users] charge and ionization state at pH 6.5

On 5/16/12 7:13 AM, Acoot Brett wrote: Dear All, Will you please tell me how GROMACS calculates the total charge of a protein at pH 6.5? And how do we assign the ionization state of the residues, especially for HIS at pH 6.5? Gromacs does not automatically deal with anything aside from pH 7 p

[gmx-users] charge and ionization state at pH 6.5

Dear All, Will you please tell me how GROMACS calculates the total charge of a protein at pH 6.5? And how do we assign the ionization state of the residues, especially for HIS at pH 6.5? I am looking forward to getting a reply from you. Cheers, Acoot-- gmx-users mailing listgmx-users@gro

Re: [gmx-users] Charge derrivation for OPLSAA forcefield

On Tue, 2012-05-08 at 11:38 -0700, Milinda Samaraweera wrote: > Hi Guys > > > I was using the program http://q4md-forcefieldtools.org/RED/ to > derrive ESP based charges for some molecules that I study. Is this a > correct method to do so if not please let me know what are the other > methods th

[gmx-users] Charge derrivation for OPLSAA forcefield

Hi Guys I was using the program http://q4md-forcefieldtools.org/RED/ to derrive ESP based charges for some molecules that I study. Is this a correct method to do so if not please let me know what are the other methods that are available. thanks alot   Milinda Samaraweera University of Connecti

Re: [gmx-users] Charge delocalization fullerene

Your statement of regret contradicts with the consciousness behind your action, which is actually underlined by that statement... Besides, maybe noone knew a good answer to your question. Try to elaborate on it and add what you could find yourself in the time since your previous post. Cheers, Ts

[gmx-users] Charge delocalization fullerene

Dear all, Sorry for spamming. > > I am trying to delocalize a charge over all the carbon atoms of a fullerene. > Up to now I just put 1/60 on each and a contra-ion far away from the bucky > ball. I do not believe this is the best approach but I can not think on a > better solution as I started

[gmx-users] Charge delocalization fullerene

 Dear all, I am trying to realistically de-localize a charge over all the carbon atoms of a fullerene. Up to now I just put 1/60 on each and a contra-ion far away from the bucky ball. I do not believe this is the best approach but i can not think on a better solution as I started with gromacs tw

Re: [gmx-users] Charge groups for particle insertion

You cannot overcome it, unless you rewrite the code. IIRC, the TPI(C) code only accepts molecules for insertion in the same charge group, as it is stated in the error. Best, João On Fri, Mar 9, 2012 at 11:05 PM, Tina Wang wrote: > I'm encountering a problem in implementing particle insertion of

[gmx-users] Charge groups for particle insertion

I'm encountering a problem in implementing particle insertion of carbon dioxide in a nanoparticle system. I'm using tabulated potentials, in which I constructed two separate tables (one for nanoparticle-carbon potentials and one for nanoparticle-oxygen potentials). The groomp command required the c

[gmx-users] Charge distribution in the topology file

Dear Gromacs Users! I want to perform in vacuum simulation for the simple peptid parametrised by Amber 99SB and Gromos 43.1 force fields. As I understoon the primary foal of in vacum simulation in the turn of all charges in the residues wich are not exposed to the solvent. >From topology file

Re: [gmx-users] Charge fitting

On 2012-01-01 10:11, parto haghighi wrote: Dear GMX usesr, I have to do charge fitting for a small molecule like ethanol. I have applied PRODRG to generate .gro and .itp for ethanol but it has wrong atomic charge. To correct it I have to use gromos 43a1 force field parameters to assign charges o

[gmx-users] Charge fitting

Dear GMX usesr, I have to do charge fitting for a small molecule like ethanol. I have applied PRODRG to generate .gro and .itp for ethanol but it has wrong atomic charge. To correct it I have to use gromos 43a1 force field parameters to assign charges on each atom (Is it right?) I have red a pape

Re: [gmx-users] charge assignment for the anomeric carbon in 53a6 ff

Yun Shi wrote: Thanks again. Since I am running MD simulation on a public cluster, I cannot modify atomtypes.atp and ffnonbonded.itp on that cluster. You can make local copies in your working directory and call that force field when running grompp. But I could get every parameter ready

Re: [gmx-users] charge assignment for the anomeric carbon in 53a6 ff

Thanks again. Since I am running MD simulation on a public cluster, I cannot modify atomtypes.atp and ffnonbonded.itp on that cluster. But I could get every parameter ready and prepare the xxx.tpr files locally, and pass them to the cluster. So the practical question is, does the tpr file contain

Re: [gmx-users] charge assignment for the anomeric carbon in 53a6 ff

Yun Shi wrote: Hi Justin, Thanks a lot for the replies. I wonder what are the "newer versions" you indicated, but I find one as: /A reoptimized GROMOS force field for hexopyranose-based carbohydrates accounting for the relative free energies of ring conformers, anomers, epimers, hydro

Re: Re: [gmx-users] charge assignment for the anomeric carbon in 53a6 ff

Hi Justin, Thanks a lot for the replies. I wonder what are the "newer versions" you indicated, but I find one as: *A reoptimized GROMOS force field for hexopyranose-based carbohydrates accounting for the relative free energies of ring conformers, anomers, epimers, hydroxymethyl rotamers, and glyc

Re: [gmx-users] charge assignment for the anomeric carbon in 53a6 ff

Yun Shi wrote: Hi all, I am doing MD simulation of some carbohydrate-protein complex with this 53a6 force-field. I noted that in any oligosaccharide, the charge assigned for anomeric carbon is 0.232 while C5 (i.e. in a non-terminal mannopyranose) is 0.376. This is kind of counter-intuitiv

[gmx-users] charge assignment for the anomeric carbon in 53a6 ff

Hi all, I am doing MD simulation of some carbohydrate-protein complex with this 53a6 force-field. I noted that in any oligosaccharide, the charge assigned for anomeric carbon is 0.232 while C5 (i.e. in a non-terminal mannopyranose) is 0.376. This is kind of counter-intuitive for me since the anom

Re: [gmx-users] Charge groups in Charmm for lipids

The new GROMACS 4.5.4 version of the CHARMM36 force field files are now uploaded on the GROMACS website contributions section. Just to note that if anyone downloaded the 4.5.4 version uploaded a few hours ago then the atomtypes.atp file was incomplete and should download this new version. Sorr

Re: [gmx-users] Charge groups in Charmm for lipids

Sure, I will upload a GROMACS 4.5.4 version of the force field files to the website. Cheers Tom On 06/08/11 01:34, Peter C. Lai wrote: On 2011-08-05 06:48:09PM -0500, Thomas Piggot wrote: Hi, Yes, this was done on purpose to reflect the different use of charge groups in CHARMM and GROMACS.

Re: [gmx-users] Charge groups in Charmm for lipids

On 2011-08-05 06:48:09PM -0500, Thomas Piggot wrote: > Hi, > > Yes, this was done on purpose to reflect the different use of charge groups > in CHARMM and GROMACS. Check out the mailing list archives for more details > about this. > > On another note you might like to take a look at the contrib

Re: [gmx-users] Charge groups in Charmm for lipids

Thanks a lot, I will check that out. From: Thomas Piggot To: Discussion list for GROMACS users Sent: Friday, August 5, 2011 6:48 PM Subject: Re: [gmx-users] Charge groups in Charmm for lipids Hi, Yes, this was done on purpose to reflect the different use of

Re: [gmx-users] Charge groups in Charmm for lipids

Hi, Yes, this was done on purpose to reflect the different use of charge groups in CHARMM and GROMACS. Check out the mailing list archives for more details about this. On another note you might like to take a look at the contributed CHARMM36 force field (available to download on the GROMACS

[gmx-users] Charge groups in Charmm for lipids

Hi, I'm making a lipid topology for DPPG in the charmm forcefield in gromacs 4.5.  I'm putting it together from pieces of what already exists as suggested in the charmm files.  I noticed that there are charge groups in the original charmm files, and these were reflected in the gromacs topology i

Re: [gmx-users] Charge group problem from pdb2gmx

Felipe Villanelo wrote: Hi everybody I want to run a EM, but grompp give me this Note: The sum of the two largest charge group radii (0.305345) is larger than rlist (1.00) - rvdw (0.90) I have read in the gmx forums, that this is a problem from the designation of charge groups,

[gmx-users] Charge group problem from pdb2gmx

Hi everybody I want to run a EM, but grompp give me this Note: The sum of the two largest charge group radii (0.305345) is larger than rlist (1.00) - rvdw (0.90) I have read in the gmx forums, that this is a problem from the designation of charge groups, but I have make the topology

Re: [gmx-users] charge groups

Also. Obviously I arranged the charge groups like this so that they would be neutral, I just didn't realise that the atoms comprising the charge groups had to be in sequence. Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> As you can see atomnr 7 HC should belong to the same charge group (1)

Re: [gmx-users] charge groups

Gavin Melaugh wrote: O.K cheers I assume that this is irrelevant in vacuum with no cut-offs Or (for reference) with PME, I would suspect, since in this case charge groups do not have to be net neutral. -Justin Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: As you can see atomnr

Re: [gmx-users] charge groups

O.K cheers I assume that this is irrelevant in vacuum with no cut-offs Gavin Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> As you can see atomnr 7 HC should belong to the same charge group (1) as >> atomnr 1&2. From the tpr file atomnr 7 (in this file 6) seems to have >> its own charge gr

Re: [gmx-users] charge groups

Gavin Melaugh wrote: As you can see atomnr 7 HC should belong to the same charge group (1) as atomnr 1&2. From the tpr file atomnr 7 (in this file 6) seems to have its own charge group (3). [atoms] ; atomnr type resnr residue namecgnr charge mass 1 CA 1 CGE

Re: [gmx-users] charge groups

As you can see atomnr 7 HC should belong to the same charge group (1) as atomnr 1&2. From the tpr file atomnr 7 (in this file 6) seems to have its own charge group (3). [atoms] ; atomnr type resnr residue namecgnr charge mass 1 CA 1 CGECA 1 -0.1

Re: [gmx-users] charge groups

Gavin Melaugh wrote: Hi Justin The two files processed.top and topol.top are the exact same. What is worrying me is that when I look at the topol.tpr from gmxdump, my charge groups do not seem to be specified the way I stated in the topology file. Can you provide a relevant snippet of the g

Re: [gmx-users] charge groups

Hi Justin The two files processed.top and topol.top are the exact same. What is worrying me is that when I look at the topol.tpr from gmxdump, my charge groups do not seem to be specified the way I stated in the topology file. Gavin Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> Hi all >>

Re: [gmx-users] charge groups

Gavin Melaugh wrote: Hi all Do atoms belonging to the same charge group have to be indexed consecutively in the topology file or can you have the following. [atoms] 1 CA 1 CGECA 1 -0.1150 12.0110 2 CB 1 CGECB 1 0.

[gmx-users] charge groups

Hi all Do atoms belonging to the same charge group have to be indexed consecutively in the topology file or can you have the following. [atoms] 1 CA 1 CGECA 1 -0.1150 12.0110 2 CB 1 CGECB 1 0. 12.0110 3 CA

Re: [gmx-users] charge group radii- use maxwarn or increase rlist?

Thank you for your helpful comments. I am totally convinced that I was not using proper force field. Best, moeed On 28 February 2011 18:12, Justin A. Lemkul wrote: > > > Moeed wrote: > >> Dear Justin, >> >> Thank you for your message. My objective is to calculate interaction >> energies betwe

Re: [gmx-users] charge group radii- use maxwarn or increase rlist?

Moeed wrote: Dear Justin, Thank you for your message. My objective is to calculate interaction energies between polymer (polyethylene) and hydrocarbon solvent ( also FE calculations). I am using rlist of 1.1 nm. 1- Do I need to increase rlist ( to 1.4 nm) to overcome the error message?

Re: [gmx-users] charge group radii- use maxwarn or increase rlist?

Dear Justin, Thank you for your message. My objective is to calculate interaction energies between polymer (polyethylene) and hydrocarbon solvent ( also FE calculations). I am using rlist of 1.1 nm. 1- Do I need to increase rlist ( to 1.4 nm) to overcome the error message? 2- As with the electro

Re: [gmx-users] charge group radii- use maxwarn or increase rlist?

Moeed wrote: Dear experts, Please kindly comment on this error. Thank you very much. I am getting the known charge group radii error. (in 4.0.7 version with the same settings my simulations run with no error) == NOTE 1 [file md.mdp]: The sum of the two largest cha

[gmx-users] charge group radii- use maxwarn or increase rlist?

Dear experts, Please kindly comment on this error. Thank you very much. I am getting the known charge group radii error. (in 4.0.7 version with the same settings my simulations run with no error) == NOTE 1 [file md.mdp]: The sum of the two largest charge group radii (0.

Re: [gmx-users] Charge groups

mohsen ramezanpour wrote: Dear All I read charge groups section in the gromacs manual. I have a question.please let me know it's answer. Is it necessary that our charge groups be made of afew number of atoms? in the other words ,if I have a charge group with 50 atom,Is my results valid? Ab

[gmx-users] Charge groups

Dear All I read charge groups section in the gromacs manual. I have a question.please let me know it's answer. Is it necessary that our charge groups be made of afew number of atoms? in the other words ,if I have a charge group with 50 atom,Is my results valid? I didn't see anywhere in manual to

Re: [gmx-users] Charge groups

mohsen ramezanpour wrote: Dear All Suppose I determined partial charges on atoms of my molecules. How can I make charge groups of them? Look for similar groups in the force field you're using, and refer to the Gromacs manual, section 4.6.2. For example I have a drug of 50 atom(of course

[gmx-users] Charge groups

Dear All Suppose I determined partial charges on atoms of my molecules. How can I make charge groups of them? For example I have a drug of 50 atom(of course along with it's hidrogenes), and all of my data for charges are as 1.3465728 (suppose they are accurate and different to eachother) Is it p

Re: [gmx-users] charge group radii larger that rlist-rvdw

Kavyashree M wrote: Dear gromacs users, I went through the papers dx.doi.org/10.1021/jp003919d . on OPLS, Its is stated in the paper "Intermolecular interactions were truncated at 11 Å, with the standard correction for the interactions beyond that radi

Re: [gmx-users] charge group radii larger that rlist-rvdw

Dear gromacs users, I went through the papers dx.doi.org/10.1021/jp003919d. on OPLS, Its is stated in the paper "Intermolecular interactions were truncated at 11 Å, with the standard correction for the interactions beyond that radius. The electrostatic interactions were quadratically feathered t

Re: [gmx-users] charge group radii larger that rlist-rvdw

Kavyashree M wrote: I went through few papers related to OPLS-AA, but could not find any specific values mentioned for vdw and coulomb intecations.. In one of the papers ".In most cases, the intermolecular nonbonded interactions were truncated at 11Å based on roughly the center-of-mass sepa

Re: [gmx-users] charge group radii larger that rlist-rvdw

I went through few papers related to OPLS-AA, but could not find any specific values mentioned for vdw and coulomb intecations.. In one of the papers ".In most cases, the intermolecular nonbonded interactions were truncated at 11Å based on roughly the center-of-mass separations with quadratic s

Re: [gmx-users] charge group radii larger that rlist-rvdw

Kavyashree M wrote: Sir, Yes sir I am using PME. And one more thing I noticed was, the protein has 7 disulphide bonds, so when I reduce all the cystine to cysteine or to alanine, the the sum of charge group radii reduces from 0.31..nm to 0.30..nm and also the value of this is identica

Re: [gmx-users] charge group radii larger that rlist-rvdw

Sir, Yes sir I am using PME. And one more thing I noticed was, the protein has 7 disulphide bonds, so when I reduce all the cystine to cysteine or to alanine, the the sum of charge group radii reduces from 0.31..nm to 0.30..nm and also the value of this is identical in case of alanine mutatio

Re: [gmx-users] charge group radii larger that rlist-rvdw

Kavyashree M wrote: Sir, System is a protein with 123 aa. No modifications were made on the pdb file, and it was submitted to pdb2gmx by removing all HETATMs, retaining only protein atoms. topology was created entirely by pdb2gmx and no other molecule was introduced. I will go t

Re: [gmx-users] charge group radii larger that rlist-rvdw

Sir, System is a protein with 123 aa. No modifications were made on the pdb file, and it was submitted to pdb2gmx by removing all HETATMs, retaining only protein atoms. topology was created entirely by pdb2gmx and no other molecule was introduced. I will go through the OPLSAA paper, but

Re: [gmx-users] charge group radii larger that rlist-rvdw

Kavyashree M wrote: Sir, What exactly can be wrong with the topology? As I tried with I don't know, what's in your system? Was the topology created entirely by pdb2gmx, or have you introduced some other molecules that you've parameterized? different PDBs of same structure at higher r

Re: [gmx-users] charge group radii larger that rlist-rvdw

Sir, What exactly can be wrong with the topology? As I tried with different PDBs of same structure at higher resolutions too, I am getting almost similar charge group radii, so can you kindly elaborate about what can go wrong in the topology to get such values? Thanks MKS On Fri, Jan 21, 2011

Re: [gmx-users] charge group radii larger that rlist-rvdw

Kavyashree M wrote: Dear gromacs users, I am using gromacs 4.5.3, OPLSAA force field, and the cut off parameters are as shown below: - ;NEIGHBOURSEARCHING PARAMETERS nstlist = 10

[gmx-users] charge group radii larger that rlist-rvdw

Dear gromacs users, I am using gromacs 4.5.3, OPLSAA force field, and the cut off parameters are as shown below: -- --- ;NEIGHBOURSEARCHING PARAMETERS nstlist = 10 10 ; FREQ

[gmx-users] charge group radii larger that rlist-rvdw

Dear gromacs users, I am using gromacs 4.5.3, OPLSAA force field, and the cut off parameters are as shown below: - ;NEIGHBOURSEARCHING PARAMETERS nstlist = 10 10 ; FREQU

Re: [gmx-users] charge group radii

On 30/11/2010 2:25 AM, Gavin Melaugh wrote: Cheers Mark for the reply I was more concerned about the Van der Waals interactions. If the distance between the centre of geometry of two charge groups is larger than rlist then these interactions are not included. I was therefore concerned if I had a

Re: [gmx-users] charge group radii

Cheers Mark for the reply I was more concerned about the Van der Waals interactions. If the distance between the centre of geometry of two charge groups is larger than rlist then these interactions are not included. I was therefore concerned if I had a situation in which certain atoms of a charge

Re: [gmx-users] charge group radii

On 26/11/2010 3:01 AM, Gavin Melaugh wrote: Hi all, I have recently been testing out the new version of Gromacs. To do so I have used files from previous simulations in Gromacs-4.0.7. When feeding the three files (mdp,gro, and top) into grompp, the following note is displayed: NOTE 3 [file pbc.

[gmx-users] charge group radii

Hi all, I have recently been testing out the new version of Gromacs. To do so I have used files from previous simulations in Gromacs-4.0.7. When feeding the three files (mdp,gro, and top) into grompp, the following note is displayed: NOTE 3 [file pbc.mdp]: The sum of the two largest charge grou

Re: [gmx-users] Charge grps and cut-off

Hi, So if I use PME for coloumb interactions, then what are my options? Would you then suggest breaking up the 12-atom charge grp in the arginine residue into 2 charge groups? Would it be enough to make the changes in the .rtp or parameters in other files must be changed? POoja On Sat, Jul 17

Re: [gmx-users] Charge grps and cut-off

Sai Pooja wrote: A charge grp consisting of 12 atoms is created from Arginine residues in my topology file. ; residue 14 ARG rtp ARG q +1.0 476NH1 14ARG N150 -0.47 14.007 ; qtot -3.47 477 H 14ARG HN150 0.31 1.00

Re: [gmx-users] Charge grps and cut-off

This is the arginine entry in the rtp file. It assigns 12 atoms to charge grp 3. [ ARG ] [ atoms ] N NH1 -0.47 0 HN H 0.310 CA CT1 0.070 HA HB 0.090 CB CT2 -0.18 1 HB1 HA 0.09

Re: [gmx-users] Charge grps and cut-off

A charge grp consisting of 12 atoms is created from Arginine residues in my topology file. ; residue 14 ARG rtp ARG q +1.0 476NH1 14ARG N150 -0.47 14.007 ; qtot -3.47 477 H 14ARG HN150 0.31 1.008 ; qtot -3.16 478

Re: [gmx-users] Charge grps and cut-off

Sai Pooja wrote: If gromacs assumes the aminoacid residues as charge groups by default then I have many residues which have 12 atoms since I am using an all-atom force field-charmm27(counting H). It doesn't matter how many atoms are in a residue, it matters how many atoms are assigned to

Re: [gmx-users] Charge grps and cut-off

If gromacs assumes the aminoacid residues as charge groups by default then I have many residues which have 12 atoms since I am using an all-atom force field-charmm27(counting H). Is there a way to define charge groups? On Sat, Jul 17, 2010 at 7:41 AM, Justin A. Lemkul wrote: > > > Sai Pooja wro

Re: [gmx-users] Charge grps and cut-off

Sai Pooja wrote: Thanks Justin. How about note 3? The largest charge group contains 12 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts.

Re: [gmx-users] Charge grps and cut-off

Thanks Justin. How about note 3? The largest charge group contains 12 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and a

Re: [gmx-users] Charge grps and cut-off

Sai Pooja wrote: Hi, This is the .mdp file that produces notes-3 and 4. However, the previous md file produces note-3. ; RUN CONTROL PARAMETERS integrator = md dt = 0.002 nsteps = 500 ; OUTPUT CONTROL OPTIONS nstxout

Re: [gmx-users] Charge grps and cut-off

Hi, This is the .mdp file that produces notes-3 and 4. However, the previous md file produces note-3. ; RUN CONTROL PARAMETERS integrator = md dt = 0.002 nsteps = 500 ; OUTPUT CONTROL OPTIONS nstxout = 0

Re: [gmx-users] Charge grps and cut-off

Sai Pooja wrote: Hi, I am trying to reproduce results from a paper which uses this cutoff. The work is on loop-folding and they use implicit solvent. I am using explicit solvent with charmm 27. Below is my mdp file. I am not sure if there is any advantage in using a large cut-off. Larg

Re: [gmx-users] Charge grps and cut-off

Hi, I am trying to reproduce results from a paper which uses this cutoff. The work is on loop-folding and they use implicit solvent. I am using explicit solvent with charmm 27. Below is my mdp file. I am not sure if there is any advantage in using a large cut-off. ; VARIOUS PREPROCESSING OPTIONS

Re: [gmx-users] Charge grps and cut-off

Sai Pooja wrote: Hi, I am getting these notes when I run grompp: NOTE 3 [file Init/ffsb_init.top]: The largest charge group contains 12 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large char

[gmx-users] Charge grps and cut-off

Hi, I am getting these notes when I run grompp: NOTE 3 [file Init/ffsb_init.top]: The largest charge group contains 12 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead

Re: [gmx-users] Charge assignment

Michael McGovern wrote: Hi everyone. I'm working on getting parameters for a protein system that has some linker residues in it. These linkers are nothing too strange, they just have some amine groups. I can get bonded parameters from the prodrg server. I know the charge groups are unr

[gmx-users] Charge assignment

Hi everyone.   I'm working on getting parameters for a protein system that has some linker residues in it.  These linkers are nothing too strange, they just have some amine groups.  I can get bonded parameters from the prodrg server.  I know the charge groups are unreliable.  I'm using the 53A6

Re: [gmx-users] charge group assignment with AMBER parameters

Jacob Spooner wrote: "Justin A. Lemkul" 3/18/2010 9:35 AM >>> Jacob Spooner wrote: I am attempting a simulation of a drug molecule using the ffamber/gaff within gromacs. When it comes to assigning charge groups the manual says that one should group together nearby atoms and the groups

Re: [gmx-users] charge group assignment with AMBER parameters

>>> "Justin A. Lemkul" 3/18/2010 9:35 AM >>> Jacob Spooner wrote: > I am attempting a simulation of a drug molecule using the ffamber/gaff within > gromacs. When it comes to assigning charge groups the manual says that one > should group together nearby atoms and the groups should have a net

Re: [gmx-users] charge group assignment with AMBER parameters

Jacob Spooner wrote: I am attempting a simulation of a drug molecule using the ffamber/gaff within gromacs. When it comes to assigning charge groups the manual says that one should group together nearby atoms and the groups should have a net integer charge. Since AMBER charge parameters are

[gmx-users] charge group assignment with AMBER parameters

I am attempting a simulation of a drug molecule using the ffamber/gaff within gromacs. When it comes to assigning charge groups the manual says that one should group together nearby atoms and the groups should have a net integer charge. Since AMBER charge parameters are obtained from QM calcu

Re: [gmx-users] Charge neutralization

Arden Perkins wrote: Hey all, I am trying to examine couplings between Mg+2 ions and a peptide with a -5 charge. I would like to optimize couplings and have considered using a +1 charge from the system. I read that GROMACS can do this and that in theory it should have the same effect as adding

[gmx-users] Charge neutralization

Hey all, I am trying to examine couplings between Mg+2 ions and a peptide with a -5 charge. I would like to optimize couplings and have considered using a +1 charge from the system. I read that GROMACS can do this and that in theory it should have the same effect as adding ions but it is not standa

Re: [gmx-users] Charge groups & Coulomb switch - artifacts in radial distribution function. Atom-based or group-based truncation?

Will Glover wrote: Hi, I have constructed a gromacs MD simulation of liquid tetrahydrofuran (at RTP) in which I'm treating each molecule as a charge group. When using a Switch for both the Coulomb and VdW interactions I see artifacts in the radial distribution function of the Oxygen--alpha-ca

[gmx-users] Charge groups & Coulomb switch - artifacts in radial distribution function. Atom-based or group-based truncation?

Hi, I have constructed a gromacs MD simulation of liquid tetrahydrofuran (at RTP) in which I'm treating each molecule as a charge group. When using a Switch for both the Coulomb and VdW interactions I see artifacts in the radial distribution function of the Oxygen--alpha-carbon (and other pair)

Re: [gmx-users] Charge group moving too much

Jennifer Williams wrote: Hello, One of my simulations just crashed after 660,000 steps with the following message: Step 660560: The charge group starting at atom 4100 moved than the distance allowed by the domain decomposition (1.50) in direction X distance out of cell 2.356293 Old coor

[gmx-users] Charge group moving too much

Hello, One of my simulations just crashed after 660,000 steps with the following message: Step 660560: The charge group starting at atom 4100 moved than the distance allowed by the domain decomposition (1.50) in direction X distance out of cell 2.356293 Old coordinates:1.7520.4

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