[gmx-users] why TIPS3P, why not TIP3P?

Hello: I noticed that the CHARMM36 FF recommend CHARMM TIP 3-point with LJ on H's model for lipids when we run pb2gmx each time. I am just wondering, why it is recommend for lipids? Is there any special superior reason to do so? As far as I google both Gromacs maillist and CHARMM forum, most

Re: [gmx-users] why TIPS3P, why not TIP3P?

CHARMM36 is a user contribution, so you should be sure to contact its author for the reason / a fix. Personally, I agree with the consensus that LJ on H is not necessary. On Jul 8, 2013 9:30 AM, "Albert" wrote: > Hello: > > I noticed that the CHARMM36 FF recommend CHARMM TIP 3-point with LJ on >

Re: [gmx-users] why TIPS3P, why not TIP3P?

In a recent benchmark by Piggot, Piñeiro and Khalid ( http://pubs.acs.org/doi/abs/10.1021/ct3003157 ), they showed that the TIP3P flavour may affect some properties (ApL) for simulations with CHARM36, concluding that CHARMM-TIP3P is recommended, at least for DPPC. I've also experienced similar

Re: [gmx-users] why TIPS3P, why not TIP3P?

On 07/08/2013 10:47 AM, Javier Cerezo wrote: In a recent benchmark by Piggot, Piñeiro and Khalid ( http://pubs.acs.org/doi/abs/10.1021/ct3003157 ), they showed that the TIP3P flavour may affect some properties (ApL) for simulations with CHARM36, concluding that CHARMM-TIP3P is recommended, at l

Re: [gmx-users] Re: problem in g_membed

On 7/7/13 10:52 PM, pavithrakb wrote: Dear Sir, Thanks so much.. now what's the solution? Should I increase the box size? Yes. If the protein protrudes "out" of the central image, then you will have an unstable system due to atomic overlap as well as violations of the minimum image convent

Re: [gmx-users] why TIPS3P, why not TIP3P?

Hi Albert I've been using the version dated July 2010, which seems to be the last one on the user contribution section. I pointed the paper by Piggot and co-workers to add a point on your original question whether CHARM-TIP3P makes a difference or not. I think that the paper answer why the d

[gmx-users] Problem creating the gro file with Amber

Hi all, I am trying to create the gromacs topology and gro file, using pdb2gmx, with the Amber99SB-ILDN ff. The problem is that my protein has two chains, but the second one, is a one residue chain, that contains a GLU. When I try it I obtain: Fatal error: In the chosen force field there is no

[gmx-users] Problem with Amber99SB-ILDN ff

I am trying to create the gromacs topology and gro file, using pdb2gmx, with the Amber99SB-ILDN ff. The problem is that my protein has two chains, but the second one, is a one residue chain, that contains a GLU. When I try it I obtain: Fatal error: In the chosen force field there is no residue

Re: [gmx-users] Problem with Amber99SB-ILDN ff

On 7/8/13 6:36 AM, Melchor S. wrote: I am trying to create the gromacs topology and gro file, using pdb2gmx, with the Amber99SB-ILDN ff. The problem is that my protein has two chains, but the second one, is a one residue chain, that contains a GLU. When I try it I obtain: Fatal error: In the

[gmx-users] Re: Problem with Amber99SB-ILDN ff

Ok, I will try it. Thank you. But when a chain starts with MET why this nomenclature is not needed? Because with MET works fine like any other forcefield. -- View this message in context: http://gromacs.5086.x6.nabble.com/Problem-with-Amber99SB-ILDN-ff-tp5009641p5009643.html Sent from the GROMA

Re: [gmx-users] Re: Problem with Amber99SB-ILDN ff

On 7/8/13 7:00 AM, Melchor S. wrote: Ok, I will try it. Thank you. But when a chain starts with MET why this nomenclature is not needed? Because with MET works fine like any other forcefield. There are a lot of variables at play here that you haven't described (Gromacs version, pdb2gmx comm

[gmx-users] Breaking of disulfisde bridges in human insulin

Dear gromacs users, I want to break two disulfide bonds of human insulin for gromacs simulation.when i used the option 'pdb2gmx -ss' only one bond was prompted for selection.If any one can help me plz reply to this mail as soon as possible. Thank you -- gmx-users mailing listgmx-users@gromac

Re: [gmx-users] Breaking of disulfisde bridges in human insulin

Hi Vinita, I would guess that the other bond would not be made anyway according to the criteria used by pdb2gmx. Or does it say it's making the bond? Does the bond appear in the .top file? Cheers, Tsjerk On 7/8/13, Vinita Kumari wrote: > Dear gromacs users, > I want to break two disulfide bond

Re: [gmx-users] Get some specific frames of traj

Thanks for your earlier suggestions. I used the command g_select -s npt_6.gro -f md_0_1.trr -select 'resname SOL and within 0.1 of (36.0, 36.0, 63.0)' -seltype res_com -selrpos res_com -os to find water molecule around a specified coordinate. But I  get this error: Input error or input inconsiste

[gmx-users] Re: Problem with Amber99SB-ILDN ff

For sure there are a lot of variable playing here, I only ask about the MET for curiosity, because I am a beginner in this kind of things we can say... I do : pdb2gmx -f pdb.pdb -p pdb.top -o pdb.gro -water spc -his -ter -posrefc 1. I don't specify nothing as separate chains or so on. I wil

Re: [gmx-users] Re: problem in g_membed

Just a piece of advices: you can consider equilibrate a lipids system which is large enough for your protein. This will save you huge amount of time on using tricks to add water later or enlarge the lipids. The system MUST BE IN PBC BOX for the g_membed input coordinate, otherwise your job w

[gmx-users] Xe atom

Hello, Please help me to add Xe atom to GROMOS96 53a6 force field. I need to carry out a protein-Xe simulation . I tried myself but failed. Thanks and Regards Divya -- View this message in context: http://gromacs.5086.x6.nabble.com/Xe-atom-tp5009650.html Sent from the GROMACS Users Forum ma

[gmx-users] remd

Sir, I did an REMD for a peptide using implicit solvent model(8 replica 10 ns each).The experimental structure of peptide in water look like betasheet(from circular dichroism). But almost all conformations from trajectory look like alpha-helices.Then how I can correlate experimental and theore

[gmx-users] umbrella sampling on GPU with Gromacs 4.6

Hello, I'd like to know if it is possible with Gromacs 4.6 to perform umbrella sampling using GPU with orientational restraints. If it is, can you give me a simple example of mdp file to see how it works? Thanks Diana -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

Re: [gmx-users] Get some specific frames of traj

On 7/8/13 7:50 AM, Shima Arasteh wrote: Thanks for your earlier suggestions. I used the command g_select -s npt_6.gro -f md_0_1.trr -select 'resname SOL and within 0.1 of (36.0, 36.0, 63.0)' -seltype res_com -selrpos res_com -os to find water molecule around a specified coordinate. But I get

Re: [gmx-users] Xe atom

On 7/8/13 9:21 AM, divyasunil wrote: Hello, Please help me to add Xe atom to GROMOS96 53a6 force field. I need to carry out a protein-Xe simulation . I tried myself but failed. Parameterization is an expert topic and requires considerable time and effort. If there are existing parameters t

Re: [gmx-users] remd

On 7/8/13 11:13 AM, Shine A wrote: Sir, I did an REMD for a peptide using implicit solvent model(8 replica 10 ns each).The experimental structure of peptide in water look like betasheet(from circular dichroism). But almost all conformations from trajectory look like alpha-helices.Then how

Re: [gmx-users] umbrella sampling on GPU with Gromacs 4.6

On 7/8/13 12:08 PM, Diana Fusco wrote: Hello, I'd like to know if it is possible with Gromacs 4.6 to perform umbrella sampling using GPU with orientational restraints. If it is, can you give me a simple example of mdp file to see how it works? As to whether or not it works, mdrun will compl

Re: [gmx-users] umbrella sampling on GPU with Gromacs 4.6

Hi Justin, I have actually followed your tutorial to perform umbrella sampling on CPU and it worked great. Can I use the same file for GPU acceleration or I have to add some fields and commands? Thanks! Diana On 7/8/13 12:47 PM, Justin Lemkul wrote: On 7/8/13 12:08 PM, Diana Fusco wrote:

Re: [gmx-users] umbrella sampling on GPU with Gromacs 4.6

On 7/8/13 12:56 PM, Diana Fusco wrote: Hi Justin, I have actually followed your tutorial to perform umbrella sampling on CPU and it worked great. Can I use the same file for GPU acceleration or I have to add some fields and commands? There's nothing GPU-specific in the .mdp file. -Justin

[gmx-users] Re: Atomtype OWT3 not found during EM step

Thanks Justin for your reply. What I actually did, I edited the .atp file by hand as follows- OWT3 15.99940 ; TIP3P WATER OXYGEN HW 1.00800 ; WATER HYDROGEN and I added those lines in the [atomtypes] section of ffnonbonded.itp file- OWT38 0.000 0.000 A 0.24889e-02

Re: [gmx-users] umbrella sampling on GPU with Gromacs 4.6

On 7/8/13 12:58 PM, Justin Lemkul wrote: On 7/8/13 12:56 PM, Diana Fusco wrote: Hi Justin, I have actually followed your tutorial to perform umbrella sampling on CPU and it worked great. Can I use the same file for GPU acceleration or I have to add some fields and commands? There's nothi

[gmx-users] Re: Atomtype OWT3 not found during EM step

Thanks Dr. Chaban for your suggestion. I included atom type in itp file. But I have know idea how do I edited pairs or triples of atoms. Would you please help me how do I fix it? -- View this message in context: http://gromacs.5086.x6.nabble.com/Atomtype-OWT3-not-found-during-EM-step-tp500952

Re: [gmx-users] Xe atom

I am a too curious person not to ask WHY Xe is of interest in connection with the protein..? Dr. Vitaly V. Chaban On Mon, Jul 8, 2013 at 6:45 PM, Justin Lemkul wrote: > > > On 7/8/13 9:21 AM, divyasunil wrote: > >> Hello, >> >> Please help me to add Xe atom to GROMOS96 53a6 force field. I nee

Re: [gmx-users] umbrella sampling on GPU with Gromacs 4.6

Great, thanks! I'll give it a try. On 7/8/13 1:02 PM, Justin Lemkul wrote: On 7/8/13 12:58 PM, Justin Lemkul wrote: On 7/8/13 12:56 PM, Diana Fusco wrote: Hi Justin, I have actually followed your tutorial to perform umbrella sampling on CPU and it worked great. Can I use the same file fo

[gmx-users] Which/What is the adequate overlap using g_BAR

Dear Gromacs People, I want to calculate free energy differences between two states A and B using g_BAR. For this I read many papers concerning the overlap between neighboring sample windows (Delta H) but I am still wondering about the following issue: I know, that there has to be an adequate ov

[gmx-users] RE: About Potential energy calculation

Hi, Won Ok, what I did was not exactly as is described. I attach the bash script that I made to do this I use the trajectory file to extract EACH frame and safe it in an independent file using trjconv . And when I do the extraction, I only extract the protein of interest, this can be done bec

[gmx-users] Stimulation stopped at 2ns

Dear All, I'm trying to do long stimulation run but every time it stops at 2ns, below pasted .mdp file parameters. How to run 10ns or more ns stimulation run? Do I need to change any parameters in .mdp file or else where. Thanks in Advance. - title = Protein-DMPC bilayer Pr

[gmx-users] g_current

Hello, I am calculating the correlation of rotational and translation dipole moment of ionic liquids. I run the 1 ns simulation and saved the trajectory at 1 fs. g_current -f md.trr -s md.tpr -n index.ndx -mc I selected "system" group. Here I pasted the initial j(t) vales and the final value is

Re: [gmx-users] Re: Atomtype OWT3 not found during EM step

On 7/8/13 1:08 PM, juganta wrote: Thanks Justin for your reply. What I actually did, I edited the .atp file by hand as follows- OWT3 15.99940 ; TIP3P WATER OXYGEN HW 1.00800 ; WATER HYDROGEN and I added those lines in the [atomtypes] section of ffnonbonded.itp file- OWT3

Re: [gmx-users] Stimulation stopped at 2ns

On 7/8/13 4:33 PM, Rama wrote: Dear All, I'm trying to do long stimulation run but every time it stops at 2ns, below pasted .mdp file parameters. How to run 10ns or more ns stimulation run? Do I need to change any parameters in .mdp file or else where. There is nothing in the .mdp file that

RE: [gmx-users] g_current

Hi, I would say the problem is too less statistics. In the paper where the tool was introduced, a simulation of 100ns has been performed in order to achieved sufficient sampling. The order of magnitude is given due to the units. Simulate for a longer time to get rid of the noise. Calculating

Re: [gmx-users] Stimulation stopped at 2ns

Thanks Justin for your reply, I found something like this, in .log file,nsteps=100 but in .mdp file it is nsteps=500. I don't see any stdout and stderr files. ___ On Mon, Jul 8, 2013 at 3:50 PM, Justin Lemkul wrote: > > > On 7/8/13 4:3

Re: [gmx-users] Stimulation stopped at 2ns

On 7/8/13 5:08 PM, Rama Krishna Koppisetti wrote: Thanks Justin for your reply, I found something like this, in .log file,nsteps=100 but in .mdp file Then you're not using the .mdp file you think you are and the run is only scheduled for 2 ns. it is nsteps=500. I don't see any st

Re: [gmx-users] Stimulation stopped at 2ns

On 8 July 2013 22:12, Justin Lemkul wrote: > > > On 7/8/13 5:08 PM, Rama Krishna Koppisetti wrote: > >> Thanks Justin for your reply, >> >> I found something like this, in .log file,nsteps=100 but in .mdp file >> > > Then you're not using the .mdp file you think you are and the run is only >

[gmx-users] Calculating shear viscosity using none-equilibrium MD: Viscosity dependent on acceleration magnitude

Hi GMX Users, I want to calculate the shear viscosity of an ionic liquid. Thus I applied the cos-acceleration in my box. However, I found that my calculated viscosity got by "g_energy" is significantly dependent on magnitude of the acceleration. I don't know why. Even if this is a none-Newton li

RE: [gmx-users] g_current

Thanks for reply. Still I have a question why it is -inf (infinity) at the end. Nilesh > Hi, > > I would say the problem is too less statistics. In the paper where the > tool > was introduced, a simulation of 100ns has been performed in order to > achieved sufficient sampling. > > The ord