Re: [gmx-users] How to remove charge of 5e-2 ??

Daer Dr.Mark You are right,But all of them(as I know) have integer charges! the problem is simullating a system with partial charges. We absolutely have such systems. On Wed, Apr 6, 2011 at 11:22 AM, Mark Abraham wrote: > On 6/04/2011 4:45 PM, mohsen ramezanpour wrote: > > Dear Dr.Justin > > Wh

[gmx-users] Methodology Check

Greetings all, I am trying to learn/use GROMACS for evaluating ligand dockings. After some effort I managed to get a run through EM, equilibration and production with protein and water. I am now having some difficulty getting a similar run going with a ligand. I am not ready to talk about the

Re: [gmx-users] How to remove charge of 5e-2 ??

On 06/04/11, mohsen ramezanpour wrote: > Daer Dr.Mark > > You are right,But all of them(as I know) have integer charges! > the problem is simullating a system with partial charges. > We absolutely have such systems. > Read the other link I provided. 3.03e00 indicates integer charge. One n

Re: [gmx-users] How to remove charge of 5e-2 ??

Hi, No we don't. You can't have fractions of elementary particles in your molecules. Erik mohsen ramezanpour skrev 2011-04-06 09.13: Daer Dr.Mark You are right,But all of them(as I know) have integer charges! the problem is simullating a system with partial charges. We absolutely have such

Re: [gmx-users] How to remove charge of 5e-2 ??

Thank you. I read it and I understood your mean. On Wed, Apr 6, 2011 at 11:52 AM, Mark Abraham wrote: > On 06/04/11, *mohsen ramezanpour * wrote: > > Daer Dr.Mark > > You are right,But all of them(as I know) have integer charges! > the problem is simullating a system with partial charges. > We a

Re: [gmx-users] How to remove charge of 5e-2 ??

On Wed, Apr 6, 2011 at 11:53 AM, Erik Marklund wrote: > Hi, > > No we don't. You can't have fractions of elementary particles in your > molecules. > > Dear Erik Yes,You are right.It is obvious . But I wanted to simulate a part of my system.for example a part of my protein! I was wrong,we can't

Re: [gmx-users] Methodology Check

On 6/04/2011 3:54 PM, Tom Dupree wrote: Greetings all, I am trying to learn/use GROMACS for evaluating ligand dockings. After some effort I managed to get a run through EM, equilibration and production with protein and water. I am now having some difficulty getting a similar run going with a

Re: [gmx-users] How to remove charge of 5e-2 ??

mohsen ramezanpour skrev 2011-04-06 09.31: On Wed, Apr 6, 2011 at 11:53 AM, Erik Marklund > wrote: Hi, No we don't. You can't have fractions of elementary particles in your molecules. Dear Erik Yes,You are right.It is obvious . But I wanted to simul

Re: [gmx-users] help on converting charmm/cgenff parameters to gromacs

Yes, Mark is exactly correct about the glitch. I had just forgotten to change this default charge in the ffnonbonded.itp when copying from another atom. As mentioned this has no impact as these charges are never used by pdb2gmx. Cheers Tom Mark Abraham wrote: On 6/04/2011 2:51 PM, Peter C.

[gmx-users] GROMOS45ACARBO force fields in the GROMACS format.

Dear All, I would like to perform some MD of disaccharides in water using GROMACS and the new ff for sugars GROMOS45ACARBO from Hansen and unenberger(JCC, 32, 6, 2011). Does somebody have these parameters in the GROMACS format (e.g. the *.itp files) and want to share them with me. Thank you

Re: [gmx-users] help on converting charmm/cgenff parameters to gromacs

On 2011-04-06 01:49:50AM -0500, Mark Abraham wrote: > The standard CHARMM .prm files give an indication of how the parameters > will be used, so it's just a matter of converting units and taking care > of any constants. Looks like if I use http://lists.gromacs.org/pipermail/gmx-users/2010-Septem

Re: [gmx-users] How to remove charge of 5e-2 ??

hm... is it possible that there is partial charge because of terminal of zwitterions? (NH3+ and COO-) When i tried to make system with terminal of just NH3+ and COO-, there was no partial charge like 5.00. But when i used zwitterion terminal, that made the 5.05 charge of the system.. it can be

Re: [gmx-users] How to remove charge of 5e-2 ??

Hyunsik wrote: hm... is it possible that there is partial charge because of terminal of zwitterions? (NH3+ and COO-) When i tried to make system with terminal of just NH3+ and COO-, there was no partial charge like 5.00. But when i used zwitterion terminal, that made the 5.05 charge of th

Re: [gmx-users] How to remove charge of 5e-2 ??

Thank you for your help. But if you don't mind can you tell me more specifically? Actually I don't know exactly what isolated protein system is. hyun 2011. 4. 6., 오후 8:56, Justin A. Lemkul 작성: > > > Hyunsik wrote: >> hm... >> is it possible that there is partial charge because of terminal of

Re: [gmx-users] How to remove charge of 5e-2 ??

On 6/04/2011 10:03 PM, Hyunsik wrote: > Thank you for your help. > > But if you don't mind can you tell me more specifically? > > Actually I don't know exactly what isolated protein system is. The zwitterion option should only be used for a polypeptide of exactly one residue, whose termini should

Re: [gmx-users] How to remove charge of 5e-2 ??

Hyunsik wrote: Thank you for your help. But if you don't mind can you tell me more specifically? Actually I don't know exactly what isolated protein system is. If you're running pdb2gmx on a single amino acid, then some force fields have special parameters for this zwitterion. If you hav

[gmx-users] not enough space

Dear All I used mdrun for generating NVT It crashed and massage was: Trying to get md5sum: nvt-1.trr: Stale NFS file handle Trying to get md5sum: nvt-1.edr: Stale NFS file handle --- Program mdrun, VERSION 4.5.3-dev-20110310-a52f8-dirty Source

Re: [gmx-users] How to remove charge of 5e-2 ??

oh.. i have missed it ... Thank you, Justin and Mark. it's really helpful for me. Hyun 2011. 4. 6., 오후 9:16, Justin A. Lemkul 작성: > > > Hyunsik wrote: >> Thank you for your help. >> But if you don't mind can you tell me more specifically? >> Actually I don't know exactly what isolated prote

[gmx-users] Re: not enough space

Dear All I used again grompp and then mdrun with the same commands, they run successfuluy!! of course with the same error. I copy and paste the command shell when these are completed: Program mdrun, VERSION 4.5.3-dev-20110310-a52f8-dirty Source code file: /home/mohsen/src/gromacs/src/gromacs/gmxl

Re: [gmx-users] not enough space

On 6/04/2011 10:29 PM, mohsen ramezanpour wrote: Dear All I used mdrun for generating NVT It crashed and massage was: Trying to get md5sum: nvt-1.trr: Stale NFS file handle You have an intermittent problem with your Network File System. For some reason GROMACS can't keep writing to the same

Re: [gmx-users] FEP and loss of performance

I followed your suggestions and i tried to perform a MD run wit GROMACS and NAMD for dialanine peptide in a water box. The cell side cubic box was 40 A. GROMACS: With the free energy module there is a drop in gromacs performance of about 10/20 fold. Standard MD: Time: 6.693 6

[gmx-users] Help needed with hacking mdrun

Dear All, I need to hack mdrun in rather complex way and need some help from people, who understand Gromacs internals really well. My problem is the following. Each N MD steps I want to pass current coordinates and forces to custom function, which transforms them in a certain way (doesn't matter

[gmx-users] speed issue, gmx runtime estimate = f(t)

Dear all, I am trying to optimize runtimes/speed for a series of calculations i plan to do with a rather complex system. When looking at runtimes I observed one peculiar issue: the estimated runtime written to stderr by mdrun with the "-v" option keepsgrowing ... in my experience this estimate n

Re: [gmx-users] FEP and loss of performance

Hi, This doesn't sound like normal behavior. In fact, this is not what I typically observe. While there may be a small performance difference, it is probably at the level of a few percent. Certainly not a factor of more than 10. You may want to provide an mdp file and topology, etc. so someone ca

Re: [gmx-users] speed issue, gmx runtime estimate = f(t)

Michael Brunsteiner wrote: Dear all, I am trying to optimize runtimes/speed for a series of calculations i plan to do with a rather complex system. When looking at runtimes I observed one peculiar issue: the estimated runtime written to stderr by mdrun with the "-v" option keepsgrowing ... in

Re: [gmx-users] FEP and loss of performance

David Mobley wrote: Hi, This doesn't sound like normal behavior. In fact, this is not what I typically observe. While there may be a small performance difference, it is probably at the level of a few percent. Certainly not a factor of more than 10. I see about a 50% reduction in speed when

Re: [gmx-users] speed issue, gmx runtime estimate = f(t)

Hi, As Justin said, it's probably the imbalance which is causing the slowdown. You can take a look at the statistics at the end of the log file. One simple thing you could do is to compare the log file of your long, gradually slowing down run with a shorter run to see which part takes more time.

[gmx-users] Umberella sampling

Dear Dr.Justin I had asked this question before but unfortunately I didn't answered good! Instead of Pulling and separating some structures in definite distances, I located my drug in definite distances along z axis (as my initial structures for doing umbrella sampling). Am I right? The main pro

Re: [gmx-users] FEP and loss of performance

I posted my test files in: https://www.dropbox.com/link/17.-sUcJyMeEL?k=0f3b6fa098389405e7e15c886dcc83c1 This is a run for a dialanine peptide in a water box. The cell side cubic box was 40 A. The directory is organized as : TEST\ topol.top Run-00/confout.gro; Equilibrated stru

Re: [gmx-users] Umberella sampling

mohsen ramezanpour wrote: Dear Dr.Justin I had asked this question before but unfortunately I didn't answered good! Instead of Pulling and separating some structures in definite distances, I located my drug in definite distances along z axis (as my initial structures for doing umbrella sam

Re: [gmx-users] Umberella sampling

Thank you very much Dr.Justin for your important notes On Wed, Apr 6, 2011 at 8:09 PM, Justin A. Lemkul wrote: > > > mohsen ramezanpour wrote: > >> Dear Dr.Justin >> I had asked this question before but unfortunately I didn't answered >> good! >> >> Instead of Pulling and separating some struc

[gmx-users] NPT equilibration

Hello, I am having problems in carrying out a NPT equilibration of my system at 500 K. System: A 5 nm cube with peptide, Li+ ions and 2,5-dihydroxybenzoic acid anion. NVT equilibration gives expected results. When I load the npt.gro file in VMD, its seems as if the molecules have fragmented/vap

Re: [gmx-users] NPT equilibration

shivangi nangia wrote: Hello, I am having problems in carrying out a NPT equilibration of my system at 500 K. System: A 5 nm cube with peptide, Li+ ions and 2,5-dihydroxybenzoic acid anion. NVT equilibration gives expected results. When I load the npt.gro file in VMD, its seems as if th

[gmx-users] Help with using g_bar

I am trying to use g_bar to derive a PMF curve from non-equilibrium trajectory data. I am using v 4.5.4 on a Mac running OSX 10.6.7. I am using the end-to-end distance of a peptide as the co-ordinate of interest. After doing a long simulation of the peptide, I selected the frames wit

Re: [gmx-users] Help with using g_bar

Warren Gallin wrote: I am trying to use g_bar to derive a PMF curve from non-equilibrium trajectory data. I am using v 4.5.4 on a Mac running OSX 10.6.7. I am using the end-to-end distance of a peptide as the co-ordinate of interest. After doing a long simulation of the peptide, I selected t

[gmx-users] Re: NPT equilibration

> I am having problems in carrying out a NPT equilibration of my system at 500 > K. > > System: A 5 nm cube with peptide, Li+ ions and 2,5-dihydroxybenzoic acid > anion. > > NVT equilibration gives expected results. > > When I load the npt.gro file in VMD, its seems as if the molecules have > fragm

Re: [gmx-users] Help with using g_bar

On 2011-04-06, at 10:58 AM, Justin A. Lemkul wrote: > > > Warren Gallin wrote: >> I am trying to use g_bar to derive a PMF curve from non-equilibrium >> trajectory data. I am using v 4.5.4 on a Mac running OSX 10.6.7. >> I am using the end-to-end distance of a peptide as the co-ordinate of >>

Re: [gmx-users] Help with using g_bar

Warren Gallin wrote: On 2011-04-06, at 10:58 AM, Justin A. Lemkul wrote: Warren Gallin wrote: I am trying to use g_bar to derive a PMF curve from non-equilibrium trajectory data. I am using v 4.5.4 on a Mac running OSX 10.6.7. I am using the end-to-end distance of a peptide as the co-ordin

[gmx-users] PME

Hello Justin, Several days ago you answered my question about calculating nonbonded terms: Question: If I want to look at nonboded interactions only, do I have to add Coul. recip. to [ LJ (SR) + Coulomb (SR) ] ? Answer: The PME-related terms contain both solute-solvent, solvent-solvent, and

Re: [gmx-users] PME

Elisabeth wrote: Hello Justin, Several days ago you answered my question about calculating nonbonded terms: Question: If I want to look at nonboded interactions only, do I have to add Coul. recip. to [ LJ (SR) + Coulomb (SR) ] ? Answer: The PME-related terms contain both solute-solven

[gmx-users] PME

Elisabeth, You CAN, in fact calculate the contribution of the reciprocal part of the PME energy to the binding energy between two components in a heterogeneous system, its just quite tedious... say, your system is molecules A and B for which you want to know the interaction energy, and the rest

[gmx-users] Re: invalid line

dear Justin A. Lemkul, thanks for your reply. You were right. Now, it works and generates the nitrogen box. But when I type: grompp_d -f ions.mdp -c 3INC_solv.gro -p topol.top -o ions.tpr I recieve this error: source file: grompp.c, line: 362 number of coordinates in coordinate file (3INC_solv.gr

Re: [gmx-users] Re: invalid line

sarah k wrote: dear Justin A. Lemkul, thanks for your reply. You were right. Now, it works and generates the nitrogen box. But when I type: grompp_d -f ions.mdp -c 3INC_solv.gro -p topol.top -o ions.tpr I recieve this error: source file: grompp.c, line: 362 number of coordinates in coordinate

[gmx-users] stress autocorrelation function

Hello all: I need to calculate stress autocorrelation function for my polymeric system. Is there a way to calculate this using gromacs tools? Thanks, SN   -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http:

Re: [gmx-users] PME

On 6 April 2011 15:01, Michael Brunsteiner wrote: > > Elisabeth, > > You CAN, in fact calculate the contribution of the reciprocal part > of the PME energy to the binding energy between two components in > a heterogeneous system, its just quite tedious... > say, your system is molecules A and B f

Re: [gmx-users] PME

Elisabeth wrote: On 6 April 2011 15:01, Michael Brunsteiner > wrote: Elisabeth, You CAN, in fact calculate the contribution of the reciprocal part of the PME energy to the binding energy between two components in a heterogeneous system, its just q

Re: [gmx-users] PME

On 6 April 2011 19:28, Justin A. Lemkul wrote: > > > Elisabeth wrote: > > >> >> On 6 April 2011 15:01, Michael Brunsteiner > mbx0...@yahoo.com>> wrote: >> >> >>Elisabeth, >> >>You CAN, in fact calculate the contribution of the reciprocal part >>of the PME energy to the binding energy

Re: [gmx-users] PME

Elisabeth wrote: On 6 April 2011 19:28, Justin A. Lemkul > wrote: Elisabeth wrote: On 6 April 2011 15:01, Michael Brunsteiner mailto:mbx0...@yahoo.com> >> wrote: Elisabeth,

Re: [gmx-users] PME

On 7/04/2011 9:23 AM, Elisabeth wrote: On 6 April 2011 15:01, Michael Brunsteiner > wrote: Elisabeth, You CAN, in fact calculate the contribution of the reciprocal part of the PME energy to the binding energy between two components in a heterogeneou

[gmx-users] how to simulate crystals in Gromacs

Dear all, I am now trying to simulate crystals in Gromacs. What I did was to convert the original crystal structure in cif format to pdb format and then use genconf to replicate the cells and run MD. Is it proper to do it in this way? Because the structure I got after MD run was completely

Re: [gmx-users] how to simulate crystals in Gromacs

On 7/04/2011 1:55 PM, ZHANG Lu wrote: > Dear all, >I am now trying to simulate crystals in Gromacs. >What I did was to convert the original crystal structure in cif format > to pdb format and then use genconf to replicate the cells and run MD. >Is it proper to do it in this way? It's w

[gmx-users] error while loading shared libraries: libgmx.so.6

Dear all, I'm using a c++ code to handle the xtc file with 'xtcio.h', but get the error when executing it. the command I use: g++ test.cpp -o test -I/usr/local/gromacs/include/gromacs -L/usr/local/gromacs/lib -lgmx ./test Error: ./test: error while loading shared libraries: libgmx.so.6

Re: [gmx-users] help on converting charmm/cgenff parameters to gromacs

Ok I'm now getting the dreaded "Unknown bond_atomtype CG2O5" grompp fatal error. I ran pdb2gmx on a pdb of my ligand and it generated a gro and a top file: http://pastebin.com/HL3k7EPU for the gro http://pastebin.com/y6T4ir7y for the top I ran "grompp -f em.mdp -c nonanone.gro -p nonanone.top -o

Re: [gmx-users] how to simulate crystals in Gromacs

Thank you for your answer. Could you give me some advice on the size of cell box? What is the proper size if I want to do MD simulation in crystal environment? I didn't change the cell size when I convert cif file to pdb file; in other word, I didn't use editconf to produce the cell box. What I did