Re: [gmx-users] tpbconv -zeroq results all coulombic energies to zero

On 2010-12-03 08.45, BIN ZHANG wrote: Hi, all: I was trying to use "tpbconv" to modify the tpr file with the command: tpbconv -s %s.tpr -nsteps -1 -zeroq -n index -o final.tpr It basically sets the charge of one group to zero. However, when I perform mdrun -rerun, all the coulombic energies are

[gmx-users] tpbconv -zeroq results all coulombic energies to zero

Hi, all: I was trying to use "tpbconv" to modify the tpr file with the command: tpbconv -s %s.tpr -nsteps -1 -zeroq -n index -o final.tpr It basically sets the charge of one group to zero. However, when I perform mdrun -rerun, all the coulombic energies are zeros, i.e., Coulomb-(SR), Coul.-r

[gmx-users] cumulative numbers or running coordination numbers ?

Hi all, What is the standard designation (if any exists) of the function that is calculated using "g_rdf -cn"? Cumulative numbers? Running coordination numbers? Which of them is better to be used in the article? Thanks for your insights. Vitaly Dr. Vitaly V. Chaban| skype: vvchaba

[gmx-users] creat .gro; select force field

Hi users: I run pure water MD. I need to run different water models. How can i get spce.gro, which means how can i get .gro of spce water? How can i get .gro of TIP4P? If i select TIP4P water model, which force field should i select? you know, i need .top, and .top should include force fie

Re: [gmx-users] Re: individual lateral diffusion coefficients

Hi. I think that these arguments are given for short-time diffusion (D1). But at larger times all MSD curves reach the same slope, so all of them have the same brownian diffusion (D2). Then, I wonder if taking all the atoms, which means more points to average, will results in better statisti

RE: [gmx-users] Re: individual lateral diffusion coefficients

It seems to me that it will be for the reasons mentioned in the paper http://dx.doi.org/10.1063/1.2393240 By focusing on the phosphate atom, you are measuring the actual movement of the entire lipid molecule within the membrane, which is the diffusion th

Re: [gmx-users] Re: individual lateral diffusion coefficients

Dear Javier, Justin, Xavier... Thank you very much for your feedback. Finally I decided to create a group for each PO4 in my system and calculate all the individual diffusion values. I also plotted all the MSDs as a function of time and took a safe -beginfit -endfit interval for the fittings. I thi

Re: [gmx-users] Re: Note on oscillation period / time step

Robin C. Underwood wrote: Thanks for all the responses. After rechecking my top and manually inputting the [ ...types ] fields, the note remains. It is not clear to me whether I need to modify my top file or add some additional constraint (either in the top or mdp). Is it OK to have a bond

[gmx-users] Re: Note on oscillation period / time step

Thanks for all the responses. After rechecking my top and manually inputting the [ ...types ] fields, the note remains. It is not clear to me whether I need to modify my top file or add some additional constraint (either in the top or mdp). Is it OK to have a bond oscillation period of this mag

Re: [gmx-users] Note on oscillation period / time step

El 02/12/10 19:02, Justin A. Lemkul escribió: Javier Cerezo wrote: Hello. It looks like you're missing the bonded-interactions parameters. [ bonds ] ; aiaj funct *R0 Kb *121 * XX* 131 * XX* 141

Re: [gmx-users] Re: individual lateral diffusion coefficients

Dear Angel, I agree with Justin comments and I might add: Taken from the marrink-2004JPC martini paper: "Microsecond simulations of the bilayer containing 256 DPPC molecules allows the observation of truely long time diffusive behavior. At T = 323 K, the lateral diffusion rates of DPPC equals 3

Re: [gmx-users] Re: individual lateral diffusion coefficients

Javier Cerezo wrote: Thanks Justin. Do you the reason behind? I am trying following that protocol and my P curve in not as linear as All-lipid-atoms one (DPPC, FF: G53a6, t=50ns). Furthermore, regarding the linear region, the slopes are not the same. So which one do you think is more accur

Re: [gmx-users] individual lateral diffusion coefficients

Ángel Piñeiro wrote: Dear all, I aim to calculate the lateral diffusion coefficients of lipids as a function of the distance to a membrane protein using the Martini force field. For this I guess I could use the diff_mol.xvg output file of the g_msd command which provides the list of diffusio

Re: [gmx-users] Note on oscillation period / time step

Javier Cerezo wrote: Hello. It looks like you're missing the bonded-interactions parameters. [ bonds ] ; aiaj funct *R0 Kb *1 2 1 * XX* 1 3 1 * XX* 1 4 1 * XX* 1 5

Re: [gmx-users] Note on oscillation period / time step

Robin, Easiest way to get it running, with the flexible bond between O and H in methane would be to decrease the time step. I would start with half a femto second time step and see what happens. All the best Rajesh On Thu, Dec 2, 2010 at 10:11 AM, Robin C. Underwood wrote: > GMX Users: > > When

Re: [gmx-users] Note on oscillation period / time step

Hello. It looks like you're missing the bonded-interactions parameters. [ bonds ] ; aiaj funct*R0 Kb *1 2 1* XX* 1 3 1* XX* 1 4 1* XX* 1 5 1* XX* 5 6 1* XX*

[gmx-users] Note on oscillation period / time step

GMX Users: When I run grompp on methanol in water in v. 4.5.3 I get the following Note: NOTE 1 [file methanol.top, line 73]: The bond in molecule-type MET between atoms 5 OA and 6 HO has an estimated oscillational period of 9.0e-03 ps, which is less than 10 times the time step of 1.0e-03 ps

Re: [gmx-users] .pqr to .pdb

Dear Maximiliano I reproduce my .pqr file and it has coordinate files too. I performed what Tsjerk said and I could convert pqr tp pdb file successfully Thanks for all Mohsen On Thu, Dec 2, 2010 at 6:00 PM, Maximiliano Figueroa wrote: > Hi, > > if your pqr file has not coordinates, is impossible

Re: [gmx-users] Re: individual lateral diffusion coefficients

Sorry for the misspell... Thanks Justin. Do you *know* the reason behind? I am trying following that protocol and my P curve in not as linear as All-lipid-atoms one (DPPC, FF: G53a6, t=50ns). Furthermore, regarding the linear region, the slopes are not the same. So which one do you think is

Re: [gmx-users] Re: individual lateral diffusion coefficients

Thanks Justin. Do you the reason behind? I am trying following that protocol and my P curve in not as linear as All-lipid-atoms one (DPPC, FF: G53a6, t=50ns). Furthermore, regarding the linear region, the slopes are not the same. So which one do you think is more accurate? Thanks again Jav

Re: [gmx-users] proton proton transfer

Olga Ivchenko skrev 2010-12-02 13.30: Dear gromacs users, I want to simulate proton transfer between water and another small molecule in gromacs. In the end I should have the velosity of proton proton exchange. Please can you advice me which method is better to use for this in gromacs. I rea

Re: [gmx-users] Re: individual lateral diffusion coefficients

Ángel Piñeiro wrote: Hi Javier I think I saw this in several mails of this list and it is also implicit in the Justin tutorial for analysis of bilayers. I am not sure whether or not this has also been published... I do not remember any paper. I think this is reasonable for lipids in contact

Re: [gmx-users] Re: individual lateral diffusion coefficients

Hi Javier I think I saw this in several mails of this list and it is also implicit in the Justin tutorial for analysis of bilayers. I am not sure whether or not this has also been published... I do not remember any paper. I think this is reasonable for lipids in contact with membrane proteins becau

Re: [gmx-users] .pqr to .pdb

On Thu, Dec 2, 2010 at 5:58 PM, Justin A. Lemkul wrote: > > > mohsen ramezanpour wrote: > >> Dear Tsjerk >> >> some information exist in pdb file which are not peresent in pqr and vise >> versa. >> I want to convert them to eachother in a way to conclude one's information >> to the other file. >>

Re: [gmx-users] .pqr to .pdb

Hi, if your pqr file has not coordinates, is impossible convert to PDB. What is the format of the original file?. However, the PQR file normally has more atoms because add hydrogens. Can you paste a little part of your pqr and pdb? Best regards Maxi On Thu, Dec 2, 2010 at 3:24 PM, mohsen ramez

Re: [gmx-users] .pqr to .pdb

mohsen ramezanpour wrote: Dear Tsjerk some information exist in pdb file which are not peresent in pqr and vise versa. I want to convert them to eachother in a way to conclude one's information to the other file. as you know a typical pdb file has a definite colomns and each of them present

Re: [gmx-users] .pqr to .pdb

Dear Tsjerk some information exist in pdb file which are not peresent in pqr and vise versa. I want to convert them to eachother in a way to conclude one's information to the other file. as you know a typical pdb file has a definite colomns and each of them present a definite charachter(for exampl

RE: [gmx-users] proton proton transfer

Sorry for the typo below. DFT based *or* semi empirical code. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Ran Friedman Sent: 02 December 2010 15:01 To: Discussion list for GROMACS users Subject: RE: [gmx-users] proton pr

RE: [gmx-users] proton proton transfer

Hi Olga, It's not straightforward in CHARMM as well. One method is to use conjugate peak refinement, but this will only get you the potential energy surface, but there's also a force field made by Meuwly for dealing with proton transfer IIRC. Depending on the system size, you may want to use QM

Re: [gmx-users] proton proton transfer

Thnaks, Justin. Probably CHARMM is suitable for this. 2010/12/2 Justin A. Lemkul > > > Olga Ivchenko wrote: > >> Dear gromacs users, >> >> I want to simulate proton transfer between water and another small >> molecule in gromacs. In the end I should have the velosity of proton proton >> exchange

Re: [gmx-users] Re: individual lateral diffusion coefficients

Hi Ángel Can you provide a citation about the use of only PO4 atoms to calculate the diffusion constant? Is it always recommended or just with CG simulations? I'm also working on diffusion calculation and that will be interesting. By the way, regarding the index files I mentioned, it might b

Re: [gmx-users] Re: individual lateral diffusion coefficients

Hi Javier 1.- you are right! the diff_mol.xvg file I reported was from a previous attempt in which I used the whole lipid molecules with the -mol option on, instead of the PO4 beads with -mol off. Sorry for this confusion 2.- As I said above, I did attempts using both the whole molecule and the PO

Re: [gmx-users] proton proton transfer

Olga Ivchenko wrote: Dear gromacs users, I want to simulate proton transfer between water and another small molecule in gromacs. In the end I should have the velosity of proton proton exchange. Please can you advice me which method is better to use for this in gromacs. I read about umbrell

Re: [gmx-users] Re: individual lateral diffusion coefficients

Hello Ángel. Well, there are a some things that I don't understand about your calculation, but might be just a problem of mine. Here you have my comments: 1. How do you get the diff_mol.xvg file if you are not using -mol in your command line input (and you index file has broken molecules).

[gmx-users] proton proton transfer

Dear gromacs users, I want to simulate proton transfer between water and another small molecule in gromacs. In the end I should have the velosity of proton proton exchange. Please can you advice me which method is better to use for this in gromacs. I read about umbrella sampling, but may be there

[gmx-users] individual lateral diffusion coefficients

Dear all, I aim to calculate the lateral diffusion coefficients of lipids as a function of the distance to a membrane protein using the Martini force field. For this I guess I could use the diff_mol.xvg output file of the g_msd command which provides the list of diffusion coefficients for each lipi

[gmx-users] Re: individual lateral diffusion coefficients

I want to add that the MSD as a function of time (msd.xvg file) looks completely linear Greetings, Ángel Piñeiro. On Thu, 2010-12-02 at 12:45 +0100, Ángel Piñeiro wrote: > Dear all, > I aim to calculate the lateral diffusion coefficients of lipids as a > function of the distance to a membrane p

[gmx-users] Allocation memory failure with g_msd (version 4.5.X)

Hi all. I found a memory allocation problem when using g_msd in verions 4.5.1 and higher when the option -mol is enabled. Here you have the command line input: $ g_msd -f DPPC_run -s DPPC_run -n -lateral z -o D_mol -b 1 -mol And the error message: ---

Re: [gmx-users] How to suppress the error "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group"

On Dec 2, 2010, at 6:16 AM, WU Yanbin wrote: > Dear GMXers, > > I'm running a simulation of water contact angle measurement on top of > graphite surface. > Initially a water cubic box is placed on two-layer graphite surface with the > rest of the box being vacuum. The water droplet is relaxed

Re: [gmx-users] add a new force field to the pdb2gmx list

yes, I lost a forcefield.itp file. 2010/12/1 Mark Abraham > On 1/12/2010 3:55 PM, Jia Haitao wrote: > > No, I did not miss any files in direction .ff. I even add a ffpolycg.itp > in ../$GMXLIB. Is there any file like FF.dat ? > > > See pdb2gmx -h > > Mark > > > 2010/12/1 Mark Abraham > >> On

Re: [gmx-users] Restraining water

2010/12/2 Mark Abraham > On 2/12/2010 12:51 PM, Guido Polles wrote: > >> Hi, >> I know it looks a little bit strange, but i was trying to restrain >> just some water in my system. >> Now, if i put something like >> [ position_restraints ] >> ; i funct fcxfcyfcz >>11

[gmx-users] Fwd: lateral diffusion coefficients on a spherical surface

Hi, I am forwarding on a message on behalf of one of my colleagues who is having problems sending messages to the list. Please take a look his message and see if you can help him with his problem. Thank you Tom Piggot Original Message Subject:lateral diffusion coef

Antw: [gmx-users] How to suppress the error "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group"

Hello, Have you also tried this simulation with a velocity rescaling thermostat in the equilibration period? Could it be that it then would work better? Bests, Emanuel >>> WU Yanbin 02.12.10 6.16 Uhr >>> Dear GMXers, I'm running a simulation of water contact angle measurement on top of graph