[gmx-users] How x2top makes proper and improper dihedrals?

Dear all, I use x2top to get topology of a capped carbon nanotube with 168 atoms using oplsaa force field. The output information about dihedreals shows as follows. Before cleaning: 1008 dihedrals There are 252 Ryckaert-Bellemans dihedrals, 0 impropers Using my own code, I also get 100

[gmx-users] How does x2top clean dihedrals?

Dear all, Sorry that I have to post this message similar to one posted several days ago, for I have spent much time on thinking about it but still have not got a credible explanation. I use x2top to get topology of a capped carbon nanotube with 168 atoms using oplsaa force field. The output

[gmx-users] Why does x2top need to clean dihedrals?

Dear all, Nobody would like to give some clues for this question, even the developer of the x2top code? I use x2top to get topology of a capped carbon nanotube with 168 atoms using oplsaa force field. The output information about dihedreals shows as follows. Before cleaning: 1008 dihedrals T

[gmx-users] Re: Why does x2top need to clean dihedrals?

>x2top -h >Did you use the -alldih flag? For OPLS like force field all dihedrals are need, for gromos like ff only one dihedral per bond is kept, that is >why. Thanks, David. I did not use -alldih. After I used it, four dihedrals for one bond are all kept. Anyway I have got this point about th

[gmx-users] How to turn off LJ interaction between two groups?

Dear all, I want to make an ideal semipermeable membrane comprised of several hundreds of atom CM in a plane, which is fully permeable to water but resistant to NaCl. I defined atomtype CM (CM is neutral) [ atomtypes ] CM 6 12.01 0.000 A 2.22343e-03 3.434770e-06 In orde

[gmx-users] RE: strange empty space inside the system box

I suggest you first can run a system with only polymer solution in NPT ensemble. After a suitable density is reached, then you can add two graphite sheets into the equilibrated system, please set the distance between graphite and solution carefully (or trial error). Best wishes, Zhongqiao Hi,

[gmx-users] Re: Non-equilibraium MD: simulating a moving plate.

Hi, have you set comm-mode = None? If no, you can set it and try again. Zhongqiao Hu Dept of Chemical and Biomolecular Engineering National University of Singpore >Hello, >I want to simulate a rigid plate (wall) moving along one direction and >reflecting all the particles it meets

[gmx-users] Re: Non-equilibraium MD: simulating a moving

I am not sure if it works. You can try to put your system into two frozen layers which will exert a resisting force on the wall. You still need to put an acceleration on the wall. But after a steady state is reached, you will see the wall will move approximately at a constant velocity. Best wis

[gmx-users] Wheter the drift velocity has been removed from calculating the temperature?

Dear all, I wonder if the drift velocity has been removed from calculating the temperature for a non-equilibrium MD in which a directional movement for a group exists due to external force applied. One paper, entitled "Why are carbon nanotubes fast transporters of water?" (Joseph and Aluru

[gmx-users] Re: Wheter the drift velocity has been removed from calculating the temperature?

>> I wonder if the drift velocity has been removed from calculating the >> temperature for a non-equilibrium MD in which a directional movement for >> a group exists due to external force applied. > Yes it is. Please check the source code in src/mdlib/update.c Thanks, David. Then h

[gmx-users] Does One need to set comm_mode = none for an equilibrium MD to get exact MSD?

Dear all, When I run equilibrium MD simulation, I did not do anything for COM removal in .mdp file. So by default, the linear motion of COM of the whole system should be removed. In this case, the MSD calculated by g_msd should be different from that otherwise. So one needs to set comm_mode = n

[gmx-users] The negative state of a Phe molecule is not parametrized in gromos96 FF?

Dear all, I wonder if a negative Phe molecule is parametrized in gromos96 FF properly. I used pdb2gmx -f phe.pdb -o phe.gro -p phe.top -ter I selected "1: NH2" for N-terminus and "0: COO-" for C-terminus. But the phe.top obtained is not correct [ atoms ] ; nr type resnr

[gmx-users] Can I put an external force on atoms in a specific region in gromacs?

Dear all, I only know in gromacs one can put external force on a group of atom. Now I want to put an external force on atoms in a specific region. For instance, say, the box size in z direction is 10 nm, I want to put force on all atoms in region from z = 4 nm to z = 6 nm during whole simulatio

[gmx-users] Can gromacs developers write code to put an external force on atoms in a specified region in later versions?

Dear gromacs developers, As far as I know, in the latest gromacs version, one only can put an external force on a group of atoms, but can not put external force on atoms in a specific region, for instance, the region from z = 4 nm to z = 6 nm. Some other softwares like NAMD seem to have such fu

[gmx-users] How to read xtc file?

Hi, I have been thinking how to write a Fortran program to read xtc file for a long time. The gmx homepage provides a code testxtc. But when I simply compile it, some errors are shown as follows: /tmp/ifortuDk9ZY.o(.text+0x5c): In function `MAIN__': : undefined reference to `xdrfopen_' /tmp/i

[gmx-users] Re: How to read xtc file?

>Install gromacs. Then check that $(GMXHOME)/lib/$(CPU)/libxtfc.whatever >exists. >Mark Dear Mark, The gmx has been installed in our cluster. But I can not find any files related to libxtfc under /lib. That means something is lost during the installation, right? In this case, are there any ot

[gmx-users] readxtc can not get coordinates without jump?

Hi, I faced one problem when reading xtc file. Assuming my xtc file is run.xtc and the last frame no. is 1 (time step=1ps, e.g, 10 ns in total), I want to see the coordinates of the whole system without jump at frame=1, and I used the command: (1)trjconv -f run.xtc -s run.tpr -o sys_1

[gmx-users] Re: readxtc can not get coordinates without jump?

Hi, Tsjerk I see, you are right. I checked the coordinates again. Readxtc can give correct coordinates without jumps. And it seems that we should be careful when using trjconv to extract coordinates without jumps. Zhongqiao -

[gmx-users] non-intergral charge for L-alanine molecules?

I want to simulated transport of D- and L- alanine molecules. First I tried using ffg43a1 force field, but D-analine will quickly flip to L-alanine during energy minimization (I dont know why). Alternatively, I tried oplsaa force fields. That's OK without flip from D- to L-. But one problem is that

[gmx-users] FW: non-intergral charge for L-alanine molecules?

Message- From: Hu Zhongqiao Sent: 2007年6月18日 7:03 PM To: 'gmx-users@gromacs.org' Subject: RE: non-intergral charge for L-alanine molecules? Thanks a lot, Mark Abraham and David, I thought the atom charge of an ALA molecule was same as those in ALA residue of a protein molecules. Th

[gmx-users] RE: non-intergral charge for L-alanine molecules?

Thanks a lot, Mark Abraham and David, I thought the atom charge of an ALA molecule was same as those in ALA residue of a protein molecules. That's wrong. Now I can use pdb2gmx -ter to set zwitterion-type ALA. About ffG43a1, I want to ask a question which is a little ambiguous to me. According to

[gmx-users] The Lennard-Jones parameter of Na+?

Dear all, I find the Lennard-Jones parameter epsilon of Na+ in Gmx is very different from some references. In gmx, I calculated sigma(Na+)=0.258nm, epsilon(Na+)=0.0617 kJ/mol But many researchers cited a paper by Dang LX [J. Am. Chem. Soc., 1995, 117, 6954-6960] and used parameters as follows

[gmx-users] Re: The Lennard-Jones parameter of Na+? (Mark Abraham)

Dear Mark Thanks for your reply. In more detail, I used ffg43a1 force field. In the file ffG43a1nb.itp, one can find the Lennard-Jones parameters for Na+ as follows: C6=7.2063121e-05; and C12= 2.1025e-08 >From these 2 values one can get epsion(Na+)=0.0617 kJ/mol. Because the force field para

[gmx-users] How does g_msd calculate the deviation of diffusion coefficient?

Hi, Every time I use g_msd to calculate the MSD for one group, this program always output the diffusion constant like # D[ SOL] = 0.4996 (+/- 0.0366) (1e-5 cm^2/s) I know that g_msd calculates the D using the least square (LSQ) method. But I dont know how to calculate the deviation of D

[gmx-users] RE: How does g_msd calculate the deviation of diffusion

Thanks a lot. Yes, now I can reproduced this error value according to this instruction. But I think it is better if g_msd can give standard deviation using the standard procedure of LSQ, which is used by the MS Excel function LINEST. Zhongqiao > This snippet can be found by g_msd -h or on the

[gmx-users] Can the g_sas in the gmx3.3.1 give correct resarea and atomarea?

I calculated SASA using g_sas for three proteins with -r and -oa and found that the atom area for one protein is considerably larger than two others. I dont know it is due to the nature of different proteins or something incorrect for the command g_sas itself. And I checked the mailing list and fou

[gmx-users] How to set N-terminal lysine carry only +1 unit charge?

Hi, I am using amber force field in Gromacs. The protein I simulated is the lysozyme (PDBID: 1HEL). I want to set all lysine residues to be neutral. According to rules using Amber in Gromacs, neutral lysine should be named to LYN. Everything goes smoothly except the N-terminal lysine residue. I

[gmx-users] Re: How to set N-terminal lysine carry only +1 unit charge?

unitcharge? > To: Discussion list for GROMACS users > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > it could not be possible since amber force field doesn't parameterized > NLYN. alternative, use ACE/NME to cap th

[gmx-users] Problem with g_energy in Gromacs 3.3!

Dear all, I tried to use g_energy to calculate potential energy in Gromacs 3.3. But I don't know how to select after something was displayed as follows:     Select the terms you want from the following list-G96Bond G96An

[gmx-users] Problem with trjorder in 3.3.1

Dear all, I tried to used the program trjorder (in the version 3.3.1) like this:   trjorder -f xtc_4.xtc -s tpr_4.tpr -n index.ndx -o ordered.xtc -b 0 -e 10 -r 0.3   But the program always output nshell.xvg file, without ordered.xtc file. And I also tried this program in 3.2.1 using the sam

[gmx-users] How to calculate the diffusion coefficient in hydration shell?

arge to be reasonable. I guess that, from the first frame to second frame, the molecules with the same labels (r1217, for example) are not the same molecules because H2O molecules have been reordered. In this case, I can not figure out how to achieve D.   Any suggesstion are welcome. Thank you very

[gmx-users] Why RMSFs of some protein chains in my system are unreasonably large?

Dear all,   I finish a 10-ns MD simulations for a system including 16 lysozyme molecule chains, some solvents H2O molecules and 128 Cl- counter ions under PBC. When I use the command to calculate the RMSF of residues as follows:   g_rmsf -f ***.xtc -s ***.tpr -o rmsf_res.xvg (I selected 3 f

[gmx-users] Re: Why RMSFs of some protein chains in my system are unreasonably large?

> are all the lysozymes treated as one protein? in that case it might be a PBC artifact. try doing the rmsf per molecule (by running the program 16> times) and then overlaying the result.   > are you trying to crystallize it?   >David.   Thank David. I just found that it was due to jumps i

[gmx-users] How to construct topology for a Manganese-containing system?

Hi,   I want to simulate a Manganese-containing system. But the current gromacs version can not build topology for Mn. I have checked the mailing list and found some discussion. But I still can not figure out how to do it. Any experienced persion can give some clear steps for this? Thanks in

[gmx-users] How to simulate the system with 100 chains?

Hi, all,   I want to simulate a unit cell of a protein under pbc. The whole system consists of about 100 chains. In original .pdb file, some chain IDs are identical, for example, 'A' is used for different chains. When I used that file without revision, gmx showed error like that: Chain iden

[gmx-users] Can I delete Mn^2+ ion from a protein molecule and then run MD?

Dear All, I want to do MD for a protein crystal containing Mn^2+ ion. Because gromacs has not provided the force field for Mn^2+ ion, I want simply delete Mn ion and then run MD. Will this lead any consequences making the MD results unacceptable?  If so, what else should I do instead?   Z

[gmx-users] how to add potassium ions correctly?

Hi, I want to add both sodium and potassium to a protein solution. But there is always error information about potassium after I used genion to add K(K+) and set right no of molecules at the bottom of .top file: No such moleculetype K (or K+) no matter I use K or K+ as potassium name and no m

[gmx-users] Re: how to add potassium ions correctly?

Hi, Mark, thanks for your reply. After some efforts I have been successful to insert potassium using ff oplsaa. But it seems that ff g43a1 actually can not recognize K or K+. It doesnt matter, anyway I can select ff oplsaa. Zhongqiao Hu Lab E5-04-27 Tel: 65161946(O) Department of Chemical and

[gmx-users] Can we run a NPT simulation with fixed lengths in x and y direction?

Hi, everyone Can we run a NPT simulation with fixed lengths in x and y direction but with variable length in z? Zhongqiao Hu Lab E5-04-27 Tel: 65161946(O) Department of Chemical and Biomolecular Engineering National University of Singapore 117576, Singapore ___

[gmx-users] Some questions about genbox and EM

Dear all, Now I have 3 questions. 1) Do I need to use genbox to add H2O twice? In the past, I first used genbox to add H2O and then used genion to add counterion. After that is EM. But now I find, if I use genbox again after genion or even after EM, there are some additional, though very few, H

[gmx-users] Re: Some questions about genbox and EM (Tsjerk Wassenaar)

Thanks, Tsjerk > >1) Do I need to use genbox to add H2O twice? >> In the past, I first used genbox to add H2O and then used genion to add >> counterion. After that is EM. But now I find, if I use genbox again after >> genion or even after EM, there are some additional, though very few, H2O >> mol

[gmx-users] Can I run BD in water media using Gmx?

Dear users, I wonder if I can run Brownian Dynamics in water media using Gmx. Although I know we can set integrator=bd, I dont know how to set dielectric constant of water in Gmx parameter file. Anyone could give some hints for this? thanks Zhongqiao Hu Lab E5-04-27 Tel: 65161946(O) Departmen

[gmx-users] Re: Can I run BD in water media using Gmx? (Hu Zhongqiao)

for longer time scale. If Gmx can not help, it will be bad. thanks in advance, Zhongqiao Message: 1 Date: Mon, 8 Jan 2007 18:15:10 +0800 From: "Hu Zhongqiao" <[EMAIL PROTECTED]> Subject: [gmx-users] Can I run BD in water media using Gmx? To: Message-ID: <[EMAIL PROTE

[gmx-users] Re: Can I run BD in water media using Gmx?(H.J.Risselada)

Thanks, Mark and Jelger, To Jelger, But If one can run BD by setting integrator=sd, how is dielectri constant of water set in the simulation? On p141 of the Manual v3.3, there is one option epsilon_r. Does it mean BD can be run successfully if epsilon_r is set as ca. 78 for water? zhongqiao

[gmx-users] an alternating current electric field can be set or not?

I want to ask a simple question. In gmx v3.3, can one set an alternating current electric field in the input parameter file? Thanks Zhongqiao Hu Lab E5-04-27 Tel: 65161946(O) Department of Chemical and Biomolecular Engineering National University of Singapore 117576, Singapore ___

[gmx-users] Speed of MD with a uniform electric field

Dear all, I am running a MD with a uniform electric field. But the speed is very slow (estimated 40 days), compared to without electric field ( 7-8 days). I don't think it is reasonable, right. Although an external electric field will slow down the MD, this large difference is byyond my expectation

[gmx-users] Re: Speed of MD with a uniform electric field

it should not make any difference at all. are you sure that is the only difference? run gmxcheck -s1 -s2 to check it. -- David. Thanks, David, Later I found that the real reason was serioulsy heavy load in the cluster. After it is decresed, and my run is expected to be finished in a reasonabl

[gmx-users] Re:Building Topology of a Drug (using the ff of your choice)

Arneh, > How does one build a topology using a different force field (say for > instance, oplsaa)? Is there a simple way to do it, I think OpenEye (or someone else, I forget whom) has some sort of automatic parameterization tool for OPLS that automatically generates parameters. Of course, th

[gmx-users] Priority of [ pairs ] and nrexcl?

Dear all, I am asking a question about pairs and nrexcle. Although I searched the list, I can not get a clear answer. According to my understanding, if I set nrexcl =3, 1-4 interactions will be excluded. But, if I set nrexcl=3 and define some pairs at the same time, the Gmx will consider which