Re: [gmx-users] reg speed of MD

Hi Take a look to mdrun -nt flag to set the number of threads. Otherwise the default is guessed according to the description displayed by mdrun (what effectively means to take all available ones, I think). There are several related entries in the mailing list. Keep in mind that thread-based

Re: [gmx-users] Largest charge group radii for Van der Waals; Largest charge group radii for Coulomb

larger than rlist (1.20) --- Is there anyone who can help see why different version mak such problem? How to solve the problem? Thanks a lot! Tom -- Javier CEREZO BASTIDA Ph.D. Student Physical Chemistry

Re: [gmx-users] Regarding NPT Eq.

is 1 bar. Since I am continuing from 20 ps NVT equilibrated configuration, in npt.mdp I have written init_step = 1 (1*0.02 fs = 20 ps). But instead of doing all this I am not able equilibrate to 1 bar. Is there any thing wrong in my formalism. Please let me. Thank you in advance. -- Jav

Re: [gmx-users] dynamic libraries and static libraries

GROMACS? I am looking forward to getting your reply. Dialing -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tlf.(+34)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the a

Re: [gmx-users] (no subject)

* Thanx in advance Anik Anik Sen Student CSIR-Central Salt & Marine Chemicals Research Institute, Gijubhai Badheka Marg. Bhavnagar, Gujarat 364002 www.csmcri.org ======== -- Javier CEREZO BASTIDA

Re: [gmx-users] (no subject)

that but the problem persisits. *From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Javier Cerezo [j...@um.es] *Sent:* Wednesday, January 11, 2012 1:56 PM *To:* gmx-users@gromacs.org *Subject

Re: [gmx-users] A theoretical question

n't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tel: (+34)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please sea

Re: [gmx-users] Error- Atom not found in residue seq nr while adding atom

s, I did the following step= pdb2gmx -ignh -f 1ahw.pdb -o sample.pdb -p sample.top and received an error= Atom ND1 not found in residue seq.nr <http://seq.nr>. 7 while adding atom. I dont understand how do i rectify this. -- Aiswarya -- Javier CEREZO BASTIDA PhD Student Physica

Re: [gmx-users] Error- Atom not found in residue seq nr while adding atom

12:34, aiswarya pawar escribió: Hi Javier, I did tried using the swisspdb for adding missing atoms still am receiving the same error. On Wed, Apr 18, 2012 at 3:44 PM, Javier Cerezo <mailto:j...@um.es>> wrote: Your PDB structure have probably some missing atoms. Check if this i

[gmx-users] make_ndx: atomname selection

Hi all I'd like to do a selection of atom names such as: a C1 C3 C2 C4 to get an index file with 4 atoms (no other matches in the file) and then use it with g_angle to calculate the dihedral. The problem is that make_ndx does not keep the order of atoms in the resulting index file as they ar

Re: [gmx-users] Test Particle Insertion of Water

velocities from previous simulations (gro file)? If the second option is more appropriate what velocity shall I adjust to the extra water molecule? I will appreciate your reply. Steven -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tel: (+34)868887434

Re: [gmx-users] Test Particle Insertion of Water

t-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 318 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de M

Re: [gmx-users] Test Particle Insertion of Water

0.485100.0 (Mnbf/s) (MFlops) (steps/hour) Performance: 0.000 0.0000.0 Finished mdrun on node 0 Wed May 9 14:18:19 2012 Files are empty. Do you have any clue what is happening? Thank you for your time, Steven On Wed, May 9, 2012 at 1:45 PM, Javier C

Re: [gmx-users] Test Particle Insertion of Water

a200150 Coords 0 Velocities200150 Forces 0 Box 200150 Well, it looks ok. Any suggestions? On Wed, May 9, 2012 at 3:01 PM, Javier Cerezo mailto:j...@um.es>> wrote: Sorry, I saw now the command line you've post

Re: [gmx-users] Test Particle Insertion

<mailto:gmx-users@gromacs.org> http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it

Re: [gmx-users] Test Particle Insertion

ulate the total potential energy then -kTlog... of this values and then substract it? Please correct me if I am wrong. Steven On Tue, May 15, 2012 at 11:59 AM, Javier Cerezo <mailto:j...@um.es>> wrote: Hi Steven. 1. Why this value is divided by nm3? Shall I multiply it b

Re: [gmx-users] Test Particle Insertion

think U_{n+1} refers to the interaction energy of the inserte particle with the system, but maybe someone could confirm or correct. Javier El 16/05/12 11:44, Steven Neumann escribió: On Wed, May 16, 2012 at 10:28 AM, Javier Cerezo <mailto:j...@um.es>> wrote: About the red

Re: [gmx-users] Place water away from existing atoms

away from existing index file of my tube? Please, help. Steven -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tel: (+34)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

Re: [gmx-users] Regarding Gas Phase Torsional Energetics

calculate the energy at each angle or any other way is available. Thank you in advance *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tel: (+34)868887434

Re: [gmx-users] Water molecule cannot be settled

VMD, I could observe that some of the molecules facing this error split in one frame (hydrogens 7A away from oxygen) or spin around 180 degrees - it depends. 4. I tried increase vdwradii of the atoms which form my Tube so they wont overlap with water If you have any suggestions I will really appre

Re: [gmx-users] Regarding GROMACS interface with G03

INDIA. +91-9686933963.* -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tel: (+34)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromac

Re: [gmx-users] Regarding error.

happening? I would appreciate any help. Iam new in using MD and gromac in particular. Suryanarayana Seera, PhD student, HYderabad, India. -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tel: (+34)868887434 -- gmx-users mailing listgmx-users

Re: [gmx-users] top/itp file to show parameters explicitly

, Cambridge, UK +44 1223 49 4588 -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tel: (+34)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org

Re: [gmx-users] Installation of GROMACS on server

m not admin of the server, would it be possible that I install the GROMACS 4.5.5 in my account (user) or upgrade the GROMACS version? Thanks for your suggestions in advance. Sincerely, Shima -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tel: (+34)8688

Re: Fw: [gmx-users] Installation of GROMACS on server

/www.gromacs.org/Support/Mailing_Lists -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tel: (+34)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.o

Re: [gmx-users] Regarding error.

There is no GROMACS tool that repairs incomplete structures, but you can find other programs that can do it. Some of them have been previously posted in this list (try a search on it). Personally I've used Swiss PDB viewer, which is useful to add missing atoms. Javier El 06/06/12 07:42, Seera

Re: [gmx-users] Regarding error.

tein in water [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 SOL 13532 NA charge 3 /Add NA ions Thanks and regards Suryanarayana Seera, JRF, India. -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tel:

Re: [gmx-users] Gromacs + Mopac error

n/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Sup

Re: [gmx-users] Gromacs + Mopac error

un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Javier CEREZO BASTIDA Ph.D. Student Physical Chemistry Universidad de Murcia 30100, Murcia (SPAIN) T: (0034)868887434 -- gmx-us

Re: FW: [gmx-users] Gromacs + Mopac error

users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_

Re: [gmx-users] Gromacs + Mopac error

problem! Thank you. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)s

Re: [gmx-users] 1,4-interactions and pairs...again

d no [pairs] or [pairtypes] directives, the program (gmx) would generate 1,4 pairs with the parameters described in the [atomtypes] directive, right? But, at the end of the simulation, I don't see any coul-1,4 or LJ1,4 energy values in the .log file. The 1,4 pairs were generated in this case?

Re: [gmx-users] multiple pdb of same protein complex

problem? many thanks, Serdar -- Javier CEREZO BASTIDA Ph.D. Student Physical Chemistry Universidad de Murcia 30100, Murcia (SPAIN) T: (0034)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http

Re: [gmx-users] solvation shells

the name of the utility, which generates an index file for the first solvation shell, based on the distance criterion? There should be one... -- Javier CEREZO BASTIDA Ph.D. Student Physical Chemistry Universidad de Murcia 30100, Murcia (SPAIN) T: (0034)868887434 -- gmx-users mailing list

Re: [gmx-users] Re: How to restrain dihedral angles to reserve the tacticity?

(with an incorrect tacticity), your way seems not to be able yield the desirable results. Could you provide further help, please? Thanks a lot. The suggestion was assuming a good initial configuration. However, i do not have sufficient expertise to further comment on this. Cheers Abhishek -- J

Re: [gmx-users] qmmm and "real-life" meaning of null lennard-jones parameters

orry for the naivety in this, but i've only made "regular protein" MD so far. I've never done any QM/MM, but my assumption would be that you have to have some valid topology to start with. Perhaps someone else can comment on this methodological issue. -Justin -- Javier CEREZO

Re: [gmx-users] mdrun -v output

le the job is running. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tel: (+34)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Plea

Re: [gmx-users] Fast Question on g_msd

the msd based on the displacement of the center of mass of each water molecule (and then it takes the average)? Sorry, I tried to find something in the archive but I was able (or lucky) to find something. Thanks for any possible help Ivan - -- Javier CEREZO BASTIDA PhD Student Ph

Re: [gmx-users] Mopac gomacs installation

ompiled library files) in usr/local/lib even i used the CPPFLAGS Does anybody give suggestion about the wrong things that i have done ? Thanks In advance -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tel: (+34)868887434 -- gmx-users mailing list

Re: [gmx-users] Dipole moment

ks Nilesh -- Javier CEREZO BASTIDA Ph.D. Student Physical Chemistry Universidad de Murcia 30100, Murcia (SPAIN) T: (0034)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.o

Re: [gmx-users] Dipole moment

u can retrieve with g_energy. Javier El 18/10/12 20:43, Nilesh Dhumal escribió: In short, I can not save dipole moment directly. I can calculate dipole moment only using .trr file. Nilesh On 10/18/12 1:45 PM, Javier Cerezo wrote: Hi The dipole is stored in the edr file, which output frequen

Re: [gmx-users] Dipole moment

ment only using .trr file. Nilesh On 10/18/12 1:45 PM, Javier Cerezo wrote: Hi The dipole is stored in the edr file, which output frequency is controlled by "nstenergy" option in the mdp parameter file. Set it appropriately during your run (nstenergy=0.003) but keep in mind that it sh

Re: [gmx-users] What is the purpose of the [ pairs ] section?

hen can I assume that 1-5, 1-6, 1-7, etc, interactions will be taken into account (at full strength), even if such pairs are not specified in [ pairs ]? I have set gen-pairs = yes, fudgeLJ = 0.5, and fudgeQQ = 0.5. Thank you for your time! Andrew DeYoung Carnegie Mellon University -- Javier CEREZO

Re: [gmx-users] Bond force constant for GROMOS

, Felix -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Mua Murcia (Spain) Tlf.(+34)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Ion distribution around Cl fix

rps= System tau_t= 0.5 ref_t= 298 pbc= xyz DispCorr= EnerPres vdw-type= Cut-off freezegrps = Cl fix freezedim= Y Y Y Kind Regard -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (

Re: [gmx-users] regarding simulation of peptide and protein complex

Hi Rashi To me, it seems more reasonable to use "pdb2gmx" for every molecule that is supported by this utility (i.e. included in a rtp file) as it will be more likely to be FF-compliant (at least for the default rtp files) and thus compatible with your protein. PROD

Re: [gmx-users] orca and qm/mm

messenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844> -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tlf.(+34)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gr

Re: [gmx-users] A question about deuteriu order parameters graph

sn2 http://www.freeimagehosting.net/6e321 Thanks in advance -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tlf.(+34)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.g

Re: [gmx-users] A question about deuteriu order parameters graph

ch for your support Bests -------- *Da:* Javier Cerezo *A:* gmx-users@gromacs.org *Inviato:* Martedì 8 Novembre 2011 9:45 *Oggetto:* Re: [gmx-users] A question about deuteriu order parameters graph Hi Alex Deuterium order parameter is

[gmx-users] gromacs/mopac compilation: linking libmopac

efined reference errors", but related to f2c funtions: +timout.c0x105:)(:. textundefined+ 0x3c8reference) :to undefined` do_fioreference' totimer.c :`(do_fio.'text In this case, do I need to include the f2c.h file somewhere in the gromacs qmmm interface code? Could someone point

Re: [gmx-users] gromacs/mopac compilation: linking libmopac

And now I could run gromacs/mopac without errors. I guess with another compiler, this problem will not arise, but at least here is a solution for (standard?) gfortran in a x86_64 system Javier El 10/11/11 14:35, Javier Cerezo escribió: Hi all I am trying to compile gromacs with mopac but I&#

Re: [gmx-users] gromacs/mopac compilation: linking libmopac (Javier Cerezo)

other tests. Of course, place this info wherever you think it will be useful. By the way, do you have any idea about the problem to build build libmopac with ifort? Regards, Javier El 17/11/11 11:26, Gerrit Groenhof escribió: 3. Re: gromacs/mopac compilation: linking libmopac (Javier C

Re: [gmx-users] gromacs installation error

me/fftw/lib In gromacs-4.5.5 directory ./configure --enable-mpi --program-suffix=_mpi --with-fft=fftw3 in this i got the error. please help. Thanks, Aiswarya -- Javier CEREZO BASTIDA Ph.D. Student Physical Chemistry Universidad de Murcia 30100, Murcia (SPAIN) T: (0034)868887434 -- gm

Re: [gmx-users] RE: logfile size

upposed to print this stuff only according to nstlog, but the code is slightly broken here. I'll suggest a fix. Nah, the code looks fine - it should only ever print at nstlog steps. Mark -- Javier CEREZO BASTIDA Ph.D. Student Physical Chemistry Universidad de Murcia 30100, Murcia (

Re: [gmx-users] gromacs installation error

on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Javier Cerezo Sender: gmx-users-boun...@gromacs.org Date: Tue, 06 Dec 2011 13:30:55 To: Discussion list for GROMACS users Reply-To: Discussion list for GROMACS users Subject: Re: [gmx-users] gromacs installati

Re: [gmx-users] Gromos parameters for atom type OA

rameters used in Gromacs since the way to write parameters is different. My problem is that there is difference in OA type between 45a3 and 53a6 in parameters given by Gromos developers but not in the files distributed in Gromacs package. Can someone explain this? BR, Samuli Ollila -- Javie

Re: [gmx-users] analysis the results of melocular dynamics simulation

DEMY OF SCIENCES NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tlf.(+34)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

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

/S0092867412015528), they also introduced normal TIP3P water model+ CHARMM36 FF for their system. In this work, they performed 100+ us long time scaled MD simulation for a extremely large membrane protein. could anybody comment on this issue? THX a lot. Albert -- Javier CEREZO BASTIDA Ph

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

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 least for DPPC. I&#x

Re: [gmx-users] QMMM number of thread

or need other simulation package (such as Gaussian, MOPAC, GAMESS) for QM/MM part? I am looking forward your kindly advices. regards, semran ipek küskü Istanbul Medeniyet University Engineering Physics Dept. ISTANBUL-TURKEI -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de

Re: [gmx-users] Self Diffusion contant

Since the surfactants form aggregation I was expecting the MSD curve to go down. Is any explanation for that. Why? suddenly increases the MSD curve. Which is then the correct slop then! Thank you Rob -- Javier CEREZO BASTIDA Estudiante de Doctorado - Dpto. Quím

Re: [gmx-users] Martini parameters for monoolein

ology exists at this moment). It is obvious that the tail part of the molecule is similar to DOPC lipid tail, however I am not sure how to parametrize the head-group of monoolein. I would appreciate if somebody could provide a guidance on this matter. Thank you, George -- Javier CER

Re: [gmx-users] Martini parameters for monoolein

Sorry, for the mistake: not Tieleman's website, but Martini's. POPG, is an example for PG lipid. In that one, the OH-C-C-OH is represented with a P4 particle as Xavier proposed. Javier El 14/10/10 09:57, Javier Cerezo escribió: Hello George. I would inspect PG lipid head (in

Re: [gmx-users] How does g_msd calculates MSD?

the MSD versus time data using some other software (e.g., gnuplot, excel, etc.). If you're doing the latter you'll need to take a look at the code in gmx_msd.c to know how the diffusion coefficent is calculated from the slope of MSD versus time data (tog et correct units, use proper sca

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

is not request or when using previous versions (even with -mol option). Am I doing something wrong? Is there anything extra to care about when submitting g_msd from versions 4.5.X? Thanks for your attention. Javier -- Javier CEREZO BASTIDA Estudiante de Doctorado - Dpto. Q

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

function of the distance to the protein in my simulations of the whole system... probably I am doing something wrong¿? Thanks for any advice Ángel Piñeiro. -- Javier CEREZO BASTIDA Estudiante de Doctorado - Dpto. Química-Física Universidad de Murcia 30100 MURCIA (E

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

cided to give this information in my message to avoid a reply saying "try to remove jumps" ;) 4.- Yes I agree that I could do the calculation by creating an index for each lipid... I guess that is the safest way to proceed... Thanks for your reply! Ángel. On Thu, 2010-12-02 at 13:

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

Saludos, Ángel. On Thu, 2010-12-02 at 14:22 +0100, Javier Cerezo wrote: 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

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

rs/2008-January/031804.html -Justin Saludos, Ángel. On Thu, 2010-12-02 at 14:22 +0100, Javier Cerezo wrote: 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 d

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

4 1 5 1 4 1 3 1 4 1 2 1 [ system ] ; Name MET in water [ molecules ] ; Compound#mols MET 1 SOL 503 Do I need to add some sort of constraint on my methanol molecule? Thanks, Robin --

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* 14

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

3 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. *From:* gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Javier Cerezo *Sent:* Friday, 3 December 2010 2:46 AM *To:* gmx-users@gromacs.org *S

Re: [gmx-users] RE: Log files

20, Nimesh Jain escribió: How do I turn off md.log fine generation in Gromacs? Thanks -- Javier CEREZO BASTIDA Estudiante de Doctorado - Dpto. Química-Física Universidad de Murcia 30100 MURCIA (España) Tlf.(+34)868887434 -- gmx-users mailing listgmx-users@g

Re: [gmx-users] water genbox 3x3x0.8 EM not successful T not high

91791 0.0128965 0.0128789 -7.7826e-06 -0.00233479 Box-Z 0.778108 0.00343907 0.00343437 -2.07536e-06 -0.000622609 Density (SI)&nbs p; 1038.7 13.6165 13.5998 0.00778513 2.33555 Heat Capacity Cv: 12.49 J/mol K (factor = 0.000973754) -- Javier CEREZO BASTIDA Estudiante de Doctorado -

[gmx-users] Segmentation fault with g_order

ión de segmento ------- -- Javier CEREZO BASTIDA - Dpto. Química-Física Universidad de Murcia 30100 Murcia (SPAIN) Tlf.(+34)868887434 -- gmx-users mailing li

[gmx-users] generation of bilayer structures

I would like to know how Gromacs handles the coordinates out of the simulation box in the .gro file during a simulation. I guess it just replicate the coordinates inside the box by the opposite face (using PBC) but I would like to have comment about it if you know. Thanks a lot! Javier -- Javier

[gmx-users] tpi segmentation fault

it works but sometimes (apparently randomly) the calculation gets stops (as if it had entered in an infinite loop) after reading the last frame. Thanks for your attention! Javier -- Javier CEREZO BASTIDA Estudiante de Doctorado - Dpto. Química-Física Universidad de Mu

RE: [gmx-users] tpi segmentation fault

ed gromacs-4.5-betaX and it works but sometimes (apparently randomly) the calculation gets stops (as if it had entered in an infinite loop) after reading the last frame. Thanks for your attention! Javier -- Javier CEREZO BASTIDA Estudiante de Doctorado - Dpto. Química-Física Uni

[gmx-users] dihedrals potential as a expansion of cosine funtions

ven if their multiplicity varies. Could anyone help me with that? How will GROMACS-4 interpret multiply defined interaction? Many thanks! Javier -- Javier CEREZO BASTIDA Estudiante de Doctorado - Dpto. Química-Física Universidad de Murcia 30100 MURCIA (España) Tlf.(+34)868

Re: [gmx-users] Overflow problem with test-particle insertion

omacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Javier CEREZO BASTIDA Estudiante de Doctorado - Dpto. Química-Física Universidad de Murcia 30100 MURCIA (España) Tlf.(+34)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.

[gmx-users] test on g_density

Hi all. I've noticed an unexpected behaviour using g_density. I have a trajectory (with time step 2) and it is split into two subsets (using trjconv) with, lets say, even and odd steps respectively. According the the algorithm I expected that the density obtained with the original traject

Re: [gmx-users] tpic run option - potential energy meaning

Hi João I thought that the meaning of "epot" is the one you point out in your mail. So, I'm also a surprised about your test. The first thing that came to me mind is on the way you calculate the energy with a "single" steepest descent step. In your mdp file, did you use "nsteps=1" or "nst

Re: [gmx-users] order parameters of partially unsaturated chains

Hello Angel. I found a detailed description of the order parameter conventions to describe molecular axis in a paper from Heller et al (JPC, 97, 8343-8360), including the case of unsaturated carbons. It should be equivalent to the implementation in GROMAS. In practice, I don't know the be